Microcoaxial cataract surgery outcomes: comparison of 1.8 mm system and 2.2 mm system.

Science.gov (United States)

Lee, Kyung-Min; Kwon, Hyung-Goo; Joo, Choun-Ki

2009-05-01

To compare clinical outcomes of a 1.8 mm and a 2.2 mm microcoaxial cataract surgery system. Department of Ophthalmology and Visual Science, Kangnam St. Mary's Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea. In a prospective study, eyes were randomly selected to have phacoemulsification using a Stellaris system or an Intrepid Infiniti system. The initial incision size was 1.8 mm and 2.2 mm, respectively. Measured intraoperative parameters included phacoemulsification time, mean cumulative dissipated ultrasound energy (CDE), change in incision size at each step of surgery, and total volume of balanced salt solution (BSS) used. The best corrected visual acuity (BCVA), corneal astigmatism, corneal thickness, and endothelial cell count were evaluated preoperatively and postoperatively. The study evaluated 86 eyes of 78 patients (43 eyes in each group). There were no significant differences in postoperative BCVA, surgically induced astigmatism, or amount of BSS used between the 2 systems (P >.05). However, for high-density cataracts, the 1.8 mm group had a greater change between the initial incision size and the incision size after phacoemulsification (P = .019, nuclear opalescence [NO] NO3; P = .001, NO4), a longer phacoemulsification time (P = .013, NO3), greater mean CDE (P = .005, NO3; P = .001, NO4), and greater corneal endothelial cell loss (P = .003, NO4). Both systems were safe and effective in microcoaxial phacoemulsification. The 1.8 mm system performed better with cortical-type cataract and the 2.2 mm system, with high-density nuclear-type cataract.

Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

Science.gov (United States)

Świderek, Katarzyna; Arafet, Kemel; Kohen, Amnon; Moliner, Vicent

2017-03-14

Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

Science.gov (United States)

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs.

Science.gov (United States)

Lu, Mingjian; Kinchen, Jason M; Rossman, Kent L; Grimsley, Cynthia; Hall, Matthew; Sondek, John; Hengartner, Michael O; Yajnik, Vijay; Ravichandran, Kodi S

2005-02-22

CDM (CED-5, Dock180, Myoblast city) family members have been recently identified as novel, evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases . They regulate multiple processes, including embryonic development, cell migration, apoptotic-cell engulfment, tumor invasion, and HIV-1 infection, in diverse model systems . However, the mechanism(s) of regulation of CDM proteins has not been well understood. Here, our studies on the prototype member Dock180 reveal a steric-inhibition model for regulating the Dock180 family of GEFs. At basal state, the N-terminal SH3 domain of Dock180 binds to the distant catalytic Docker domain and negatively regulates the function of Dock180. Further studies revealed that the SH3:Docker interaction sterically blocks Rac access to the Docker domain. Interestingly, ELMO binding to the SH3 domain of Dock180 disrupted the SH3:Docker interaction, facilitated Rac access to the Docker domain, and contributed to the GEF activity of the Dock180/ELMO complex. Additional genetic rescue studies in C. elegans suggested that the regulation of the Docker-domain-mediated GEF activity by the SH3 domain and its adjoining region is evolutionarily conserved. This steric-inhibition model may be a general mechanism for regulating multiple SH3-domain-containing Dock180 family members and may have implications for a variety of biological processes.

Protein unfolding with a steric trap.

Science.gov (United States)

Blois, Tracy M; Hong, Heedeok; Kim, Tae H; Bowie, James U

2009-10-07

The study of protein folding requires a method to drive unfolding, which is typically accomplished by altering solution conditions to favor the denatured state. This has the undesirable consequence that the molecular forces responsible for configuring the polypeptide chain are also changed. It would therefore be useful to develop methods that can drive unfolding without the need for destabilizing solvent conditions. Here we introduce a new method to accomplish this goal, which we call steric trapping. In the steric trap method, the target protein is labeled with two biotin tags placed close in space so that both biotin tags can only be bound by streptavidin when the protein unfolds. Thus, binding of the second streptavidin is energetically coupled to unfolding of the target protein. Testing the method on a model protein, dihydrofolate reductase (DHFR), we find that streptavidin binding can drive unfolding and that the apparent binding affinity reports on changes in DHFR stability. Finally, by employing the slow off-rate of wild-type streptavidin, we find that DHFR can be locked in the unfolded state. The steric trap method provides a simple method for studying aspects of protein folding and stability in native solvent conditions, could be used to specifically unfold selected domains, and could be applicable to membrane proteins.

Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics

Science.gov (United States)

Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...

Understanding the Steric Height Long Term Variability at the Bermuda Atlantic Time-Series Study (BATS) Site with a Neutral Density Approach

Science.gov (United States)

Goncalves Neto, A.; Johnson, R. J.; Bates, N. R.

2016-02-01

Rising sea level is one of the main concerns for human life in a scenario with global atmosphere and ocean warming, which is of particular concern for oceanic islands. Bermuda, located in the center of the Sargasso Sea, provides an ideal location to investigate sea level rise since it has a long term tide gauge (1933-present) and is in close proximity to deep ocean time-series sites, namely, Hydrostation `S' (1954-present) and the Bermuda Atlantic Time-Series Study site (1988-present). In this study, we use the monthly CTD deep casts at BATS to compute the contribution of steric height (SH) to the local sea surface height (SSH) for the past 24 years. To determine the relative contribution from the various water masses we first define 8 layers (Surface Layer, Upper Thermocline, Subtropical Mode-Water, Lower Thermocline, Antarctic Intermediate Water, Labrador Sea Water, Iceland-Scotland Overflow Water, Denmark Strait Overflow Water) based on neutral density criteria for which SH is computed. Additionally, we calculate the thermosteric and halosteric components for each of the defined neutral density layers. Surprisingly, the results show that, despite a 3.3mm/yr sea level rise observed at the Bermuda tide gauge, the steric contribution to the SSH at BATS has decreased at a rate of -1.1mm/yr during the same period. The thermal component is found to account for the negative trend in the steric height (-4.4mm/yr), whereas the halosteric component (3.3mm/yr) partially compensates the thermal signal and can be explained by an overall cooling and freshening at the BATS site. Although the surface layer and the upper thermocline waters are warming, all the subtropical and polar water masses, which represent most of the local water column, are cooling and therefore drive the overall SH contribution to the local SSH. Hence, it suggests that the mass contribution to the local SSH plays an important role in the sea level rise, for which we investigate with GRACE data.

Sterically Bulky NHC Adducts of GaMe3 and InMe3 for H2 Activation and Lactide Polymerization

Directory of Open Access Journals (Sweden)

Anaëlle Bolley

2018-01-01

Full Text Available The sterically bulky Ga(III and In(III (IPr*MMe3 adducts (1 and 2 and (SItBuMMe3 adducts (3 and 4 (M = Ga, In; IPr* = 1,3-bis{2,6-bis(diphenylmethyl-4-methylphenyl}-1,3-dihydro- imidazol-2-ylidene; SItBu = 1,3-bis(1,1-dimethylethyl-imidazolidin-2-ylidene were prepared and structurally characterized, allowing an estimation of the steric hindrance of such Lewis pairs (yields in 1–4: 92%, 90%, 73%, and 42%, respectively. While the IPr* adducts 1 and 2 are robust species, the more severely congested SItBu adducts 3 and 4 are more reactive and exhibit a limited stability in solution. Adduct (SItBuGaMe3 (3 reacts quickly with H2 at room temperature to afford the corresponding aminal product, 1,3-di-tert-butylimidazolidine (5, along with free GaMe3. Such Frustrated Lewis Pair (FLP reactivity constitutes the first instance of a H2 activation involving a simple trialkyl GaR3 species. Adduct 3 also mediates the ring-opening polymerization (ROP of rac-lactide at room temperature to afford cyclic polylactide (PLA.

Fisher information and steric effect: study of the internal rotation barrier of ethane.

Science.gov (United States)

Esquivel, Rodolfo O; Liu, Shubin; Angulo, Juan Carlos; Dehesa, Jesús S; Antolín, Juan; Molina-Espíritu, Moyocoyani

2011-05-05

On the basis of a density-based quantification of the steric effect [Liu, S. B. J. Chem. Phys.2007, 126, 244103], the origin of the internal rotation barrier between the eclipsed and staggered conformers of ethane is systematically investigated in this work from an information-theoretical point of view by using the Fisher information measure in conjugated spaces. Two kinds of computational approaches are considered in this work: adiabatic (with optimal structure) and vertical (with fixed geometry). The analyses are performed systematically by following, in each case, the conformeric path by changing the dihedral angle from 0 to 180° . This is calculated at the HF, MP2, B3LYP, and CCSD(T) levels of theory and with several basis sets. Selected descriptors of the densities are utilized to support the observations. Our results show that in the adiabatic case the eclipsed conformer possesses a larger steric repulsion than the staggered conformer, but in the vertical cases the staggered conformer retains a larger steric repulsion. Our results verify the plausibility for defining and computing the steric effect in the post-Hartree-Fock level of theory according to the scheme proposed by Liu.

Tuning and Quantifying Steric and Electronic Effects of N-Heterocyclic Carbenes

KAUST Repository

Falivene, Laura

2014-07-12

This chapter states that the main handles for tuning steric and electronic effects are the substituents on N atoms, the nature of the C4-C5 bridge (either saturated or unsaturated), and the substituents on the C4 and C5 atoms. The initial intuition that steric properties of N-heterocyclic carbenes (NHCs) could be modulated and could impact catalytic behavior stimulated the development of steric descriptors to quantify the steric requirement of different NHCs and, possibly, to compare them with tertiary phosphines. NHCs can be classified as typically strong σ-basic/π-acid ligands, although they have been also shown to exhibit reasonable π-basic properties. This electronic modularity allows NHC ligands to adapt flexibly to different chemical environments represented by a transition metal and the other ligands. © 2014 Wiley-VCH Verlag GmbH & Co. KGaA. All rights reserved.

Sporadic Creutzfeldt-Jakob Disease MM1+2C and MM1 are Identical in Transmission Properties.

Science.gov (United States)

Kobayashi, Atsushi; Matsuura, Yuichi; Iwaki, Toru; Iwasaki, Yasushi; Yoshida, Mari; Takahashi, Hitoshi; Murayama, Shigeo; Takao, Masaki; Kato, Shinsuke; Yamada, Masahito; Mohri, Shirou; Kitamoto, Tetsuyuki

2016-01-01

The genotype (methionine, M or valine, V) at polymorphic codon 129 of the PRNP gene and the type (1 or 2) of abnormal prion protein in the brain are the major determinants of the clinicopathological features of sporadic Creutzfeldt-Jakob disease (CJD), thus providing molecular basis for classification of sporadic CJD, that is, MM1, MM2, MV1, MV2, VV1 or VV2. In addition to these "pure" cases, "mixed" cases presenting mixed neuropathological and biochemical features have also been recognized. The most frequently observed mixed form is the co-occurrence of MM1 and MM2, namely MM1+2. However, it has remained elusive whether MM1+2 could be a causative origin of dura mater graft-associated CJD (dCJD), one of the largest subgroups of iatrogenic CJD. To test this possibility, we performed transmission experiments of MM1+2 prions and a systematic neuropathological examination of dCJD patients in the present study. The transmission properties of the MM1+2 prions were identical to those of MM1 prions because MM2 prions lacked transmissibility. In addition, the neuropathological characteristics of MM2 were totally absent in dCJD patients examined. These results suggest that MM1+2 can be a causative origin of dCJD and causes neuropathological phenotype similar to that of MM1. © 2015 International Society of Neuropathology.

Direct access to highly crystalline mesoporous nano TiO2 using sterically bulky organic acid templates

Science.gov (United States)

Bakre, Pratibha V.; Tilve, S. G.

2018-05-01

Sterically bulky monocarboxylic acid templates pivalic acid and phenoxyacetic acid are reported for the first time as organic templates in the sol-gel synthesis of TiO2. Mesoporous nanoparticulates of pure anatase phase and of well defined size were synthesized. The characterization of the materials prepared was done by various methods such as XRD, SEM, TEM, FTIR, UV-DRS, BET, etc. The prepared TiO2 samples were evaluated for the day light photodegradation of methylene blue by comparing with Degussa P25 and templates free synthesized TiO2 and were found to be more efficient.

Substituent effects in heterogeneous catalysis--5. The steric hindrance of bulky alkyl substituents in cyclohexanone hydrogenation

Energy Technology Data Exchange (ETDEWEB)

Chihara, T; Tanaka, K

1979-02-01

The steric hindrance of bulky alkyl substituents in cyclohexanone hydrogenation was demonstrated by the reactivities of 2-isopropyl and 2-tert.-butyl cyclohexanone relative to cyclohexanone in individual and competitive hydrogenation at 30/sup 0/C over alumina-supported ruthenium, rhodium, and platinum catalysts. The results indicate that the ketone adsorption onto the catalyst is sterically hindered by the alkyl substitution significantly more than the surface reaction which follows the adsorption.

Sterically controlled mechanochemistry under hydrostatic pressure

Science.gov (United States)

Yan, Hao; Yang, Fan; Pan, Ding; Lin, Yu; Hohman, J. Nathan; Solis-Ibarra, Diego; Li, Fei Hua; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Tkachenko, Boryslav A.; Fokin, Andrey A.; Schreiner, Peter R.; Galli, Giulia; Mao, Wendy L.; Shen, Zhi-Xun; Melosh, Nicholas A.

2018-02-01

Mechanical stimuli can modify the energy landscape of chemical reactions and enable reaction pathways, offering a synthetic strategy that complements conventional chemistry. These mechanochemical mechanisms have been studied extensively in one-dimensional polymers under tensile stress using ring-opening and reorganization, polymer unzipping and disulfide reduction as model reactions. In these systems, the pulling force stretches chemical bonds, initiating the reaction. Additionally, it has been shown that forces orthogonal to the chemical bonds can alter the rate of bond dissociation. However, these bond activation mechanisms have not been possible under isotropic, compressive stress (that is, hydrostatic pressure). Here we show that mechanochemistry through isotropic compression is possible by molecularly engineering structures that can translate macroscopic isotropic stress into molecular-level anisotropic strain. We engineer molecules with mechanically heterogeneous components—a compressible (‘soft’) mechanophore and incompressible (‘hard’) ligands. In these ‘molecular anvils’, isotropic stress leads to relative motions of the rigid ligands, anisotropically deforming the compressible mechanophore and activating bonds. Conversely, rigid ligands in steric contact impede relative motion, blocking reactivity. We combine experiments and computations to demonstrate hydrostatic-pressure-driven redox reactions in metal-organic chalcogenides that incorporate molecular elements that have heterogeneous compressibility, in which bending of bond angles or shearing of adjacent chains activates the metal-chalcogen bonds, leading to the formation of the elemental metal. These results reveal an unexplored reaction mechanism and suggest possible strategies for high-specificity mechanosynthesis.

SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps

KAUST Repository

Falivene, Laura; Credendino, Raffaele; Poater, Albert; Petta, Andrea; Serra, Luigi; Oliva, Romina; Scarano, Vittorio; Cavallo, Luigi

2016-01-01

Developing more efficient catalysts remains one of the primary targets of organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present a Web application for analyzing the catalytic pocket of metal complexes using topographic steric maps as a general and unbiased descriptor that is suitable for every class of catalysts. To show the broad applicability of our approach, we first compared the steric map of a series of transition metal complexes presenting popular mono-, di-, and tetracoordinated ligands and three classic zirconocenes. This comparative analysis highlighted similarities and differences between totally unrelated ligands. Then, we focused on a recently developed Fe(II) catalyst that is active in the asymmetric transfer hydrogenation of ketones and imines. Finally, we expand the scope of these tools to rationalize the inversion of enantioselectivity in enzymatic catalysis, achieved by point mutation of three amino acids of mononuclear p-hydroxymandelate synthase.

SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps

KAUST Repository

Falivene, Laura

2016-06-27

Developing more efficient catalysts remains one of the primary targets of organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present a Web application for analyzing the catalytic pocket of metal complexes using topographic steric maps as a general and unbiased descriptor that is suitable for every class of catalysts. To show the broad applicability of our approach, we first compared the steric map of a series of transition metal complexes presenting popular mono-, di-, and tetracoordinated ligands and three classic zirconocenes. This comparative analysis highlighted similarities and differences between totally unrelated ligands. Then, we focused on a recently developed Fe(II) catalyst that is active in the asymmetric transfer hydrogenation of ketones and imines. Finally, we expand the scope of these tools to rationalize the inversion of enantioselectivity in enzymatic catalysis, achieved by point mutation of three amino acids of mononuclear p-hydroxymandelate synthase.

Mechanical Design of HD2, a 15 T Nb3Sn Dipole Magnet with a 35 mm Bore

Energy Technology Data Exchange (ETDEWEB)

Ferracin, P.; Bartlett, S.E.; Caspi, S.; Dietderich, D.R.; Gourlay, S.A.; Hafalia, A.R.; Hannaford, C.R.; Lietzke, A.F.; Mattafirri, S.; McInturff, A.D.; Sabbi, G.L.

2006-06-01

After the fabrication and test of HD1, a 16 T Nb{sub 3}Sn dipole magnet based on flat racetrack coil configuration, the Superconducting Magnet Program at Lawrence Berkeley National Laboratory (LBNL) is developing the Nb{sub 3}Sn dipole HD2. With a dipole field above 15 T, a 35 mm clear bore, and nominal field harmonics within a fraction of one unit, HD2 represents a further step towards the application of block-type coils to high-field accelerator magnets. The design features tilted racetrack-type ends, to avoid obstructing the beam path, and a 4 mm thick stainless steel tube, to support the coil during the preloading operation. The mechanical structure, similar to the one used for HD1, is based on an external aluminum shell pretensioned with pressurized bladders. Axial rods and stainless steel plates provide longitudinal support to the coil ends during magnet excitation. A 3D finite element analysis has been performed to evaluate stresses and deformations from assembly to excitation, with particular emphasis on conductor displacements due to Lorentz forces. Numerical results are presented and discussed.

Comparative study of PBI Cross Linked Utilizing Agents of Varying Steric Configurations

DEFF Research Database (Denmark)

Kirkebcek, Andreas; Aili, David; Li, Qingfeng

2016-01-01

ionic or covalent cross linking. When considering such, little attention is devoted to explore the effect of the sterical configuration of the cross linking agent. In this contribution three different cross linking agents are utilized to evaluate how these affects final membrane properties.......The high thermal and chemical stability of poly[2,2'-(m-phenylene)-5,5' bibenzimidazole] (PBI) accounts for its wise spread use in high temperature polymer electrolyte membrane fuel cells (HT- PEMFC). By doping the membrane with phosphoric acid (PA) ionic conductivity is obtained. Thus conductivity...... is dependent on the amount of PA present within the membrane. However mechanical properties are reduced are significantly reduced due to the plasticizing effect shown by PA [1]. This effect is due to PBI chain displacement. This effect can be lessened by use of cross linking [2-4]. This can be obtained using...

Poisson-Nernst-Planck equations with steric effects - non-convexity and multiple stationary solutions

Science.gov (United States)

Gavish, Nir

2018-04-01

We study the existence and stability of stationary solutions of Poisson-Nernst-Planck equations with steric effects (PNP-steric equations) with two counter-charged species. We show that within a range of parameters, steric effects give rise to multiple solutions of the corresponding stationary equation that are smooth. The PNP-steric equation, however, is found to be ill-posed at the parameter regime where multiple solutions arise. Following these findings, we introduce a novel PNP-Cahn-Hilliard model, show that it is well-posed and that it admits multiple stationary solutions that are smooth and stable. The various branches of stationary solutions and their stability are mapped utilizing bifurcation analysis and numerical continuation methods.

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.

Science.gov (United States)

Acevedo, Orlando; Jorgensen, William L

2010-01-19

Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty

Steric effects in release of amides from linkers in solid-phase synthesis. Molecular mechanics modeling of key step in peptide and combinatorial chemistry

DEFF Research Database (Denmark)

Norrby, Per-Ola; Jensen, Knud Jørgen

2006-01-01

Acidolytic release of an amide from a solid support by C-N bond cleavage is all ubiquitous and crucial step in many solid-phase syntheses. We have used molecular modeling of a pseudo-equilibrium to explore substituent and steric effects in the release of peptides. The high acid-lability of the ba......Acidolytic release of an amide from a solid support by C-N bond cleavage is all ubiquitous and crucial step in many solid-phase syntheses. We have used molecular modeling of a pseudo-equilibrium to explore substituent and steric effects in the release of peptides. The high acid......-lability of the backbone amide linkage (BAL), which releases sec. amides, compared to C-terminal amide anchoring, which releases primary amides, was rationalized by steric relief upon cleavage. Thus, the relative stability of the carbenium ion formed from the linker in the acidolytic release is an insufficient measure...

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex.

Science.gov (United States)

Dohn, A O; Jónsson, E Ö; Levi, G; Mortensen, J J; Lopez-Acevedo, O; Thygesen, K S; Jacobsen, K W; Ulstrup, J; Henriksen, N E; Møller, K B; Jónsson, H

2017-12-12

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H 2 O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt 2 (P 2 O 5 H 2 ) 4 ] 4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

2016 IFToMM Asian Conference on Mechanism and Machine Science (IFToMM Asian MMS 2016) & 2016 International Conference on Mechanism and Machine Science (CCMMS 2016)

CERN Document Server

Wang, Nianfeng; Huang, Yanjiang

2017-01-01

These proceedings collect the latest research results in mechanism and machine science, intended to reinforce and improve the role of mechanical systems in a variety of applications in daily life and industry. Gathering more than 120 academic papers, it addresses topics including: Computational kinematics, Machine elements, Actuators, Gearing and transmissions, Linkages and cams, Mechanism design, Dynamics of machinery, Tribology, Vehicle mechanisms, dynamics and design, Reliability, Experimental methods in mechanisms, Robotics and mechatronics, Biomechanics, Micro/nano mechanisms and machines, Medical/welfare devices, Nature and machines, Design methodology, Reconfigurable mechanisms and reconfigurable manipulators, and Origami mechanisms. This is the fourth installment in the IFToMM Asian conference series on Mechanism and Machine Science (ASIAN MMS 2016). The ASIAN MMS conference initiative was launched to provide a forum mainly for the Asian community working in Mechanism and Machine Science, in order to ...

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex

DEFF Research Database (Denmark)

Dohn, A. O.; Jónsson, E. Ö.; Levi, Gianluca

2017-01-01

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory...... and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds...

Multiple solutions of steady-state Poisson–Nernst–Planck equations with steric effects

International Nuclear Information System (INIS)

Lin, Tai-Chia; Eisenberg, Bob

2015-01-01

Experiments measuring currents through single protein channels show unstable currents. Channels switch between ‘open’ or ‘closed’ states in a spontaneous stochastic process called gating. Currents are either (nearly) zero or at a definite level, characteristic of each type of protein, independent of time, once the channel is open. The steady state Poisson–Nernst–Planck equations with steric effects (PNP-steric equations) describe steady current through the open channel quite well, in a wide variety of conditions. Here we study the existence of multiple solutions of steady state PNP-steric equations to see if they themselves, without modification or augmentation, can describe two levels of current. We prove that there are two steady state solutions of PNP-steric equations for (a) three types of ion species (two types of cations and one type of anion) with a positive constant permanent charge, and (b) four types of ion species (two types of cations and their counter-ions) with a constant permanent charge but no sign condition. The excess currents (due to steric effects) associated with these two steady state solutions are derived and expressed as two distinct formulas. Our results indicate that PNP-steric equations may become a useful model to study spontaneous gating of ion channels. Spontaneous gating is thought to involve small structural changes in the channel protein that perhaps produce large changes in the profiles of free energy that determine ion flow. Gating is known to be modulated by external structures. Both can be included in future extensions of our present analysis. (paper)

Metal coordination by sterically hindered heterocyclic ligands, including 2-vinylpyridine, assessed by investigation of cobaloximes.

Science.gov (United States)

Siega, Patrizia; Randaccio, Lucio; Marzilli, Patricia A; Marzilli, Luigi G

2006-04-17

Structural and 1H NMR data have been obtained for cobaloximes with the bulkiest substituted pyridines reported so far. We have isolated in noncoordinating solvents the complexes CH3Co(DH)2L (methylcobaloxime, where DH = the monoanion of dimethylglyoxime) with L = sterically hindered N-donor ligands: quinoline, 4-CH3quinoline, 2,4-(CH3)2pyridine, and 2-R-pyridine (R = CH3, OCH3, CH2CH3, CH=CH2). We have found that the Co-N(ax) bond is very long in the structurally characterized complexes. In particular, CH3Co(DH)2(4-CH3quinoline) has a longer Co-N(ax) bond (2.193(3) A) than any reported for methylcobaloximes. The main cause of the long bonds is unambiguously identified as the steric bulk of L by the fairly linear relationship found for Co-N(ax) distance vs CCA (calculated cone angle, CCA, a computed measure of bulk) over an extensive series of methylcobaloximes. The linear relationship improves if L basicity (quantified by pKa) is taken into account. In anhydrous CDCl3 at 25 degrees C, all complexes except the 2-aminopyridine adduct exhibit 1H NMR spectra consistent with partial dissociation of L to form the methylcobaloxime dimer. 1H NMR experiments at -20 degrees C allowed us to assess qualitatively the relative binding ability of L as follows: 2,4-(CH3)2pyridine > 4-CH3quinoline approximately = quinoline approximately = 2-CH3pyridine > 2-CH3Opyridine > 2-CH3CH2pyridine > 2-CH2=CHpyridine. The broadness of the 1H NMR signals at 25 degrees C suggests a similar order for the ligand exchange rate. The lack of dissociation by 2-aminopyridine is attributed to an intramolecular hydrogen bond between the NH2 group and an oxime O atom. The weaker than expected binding of 2-vinylpyridine relative to the Co-N(ax) bond length is attributed to rotation of the 2-vinyl group required for this bulky ligand to bind to the metal center, a conclusion supported by pronounced changes in 2-vinylpyridine signals upon coordination.

Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model.

Science.gov (United States)

Wang, Bo; Truhlar, Donald G

2013-02-12

Tuned and balanced redistributed charge schemes have been developed for modeling the electrostatic fields of bonds that are cut by a quantum mechanical-molecular mechanical boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. First, the charge is balanced by adjusting the charge on the MM boundary atom to conserve the total charge of the entire QM/MM system. In the balanced smeared redistributed charge (BSRC) scheme, the adjusted MM boundary charge is smeared with a smearing width of 1.0 Å and is distributed in equal portions to the midpoints of the bonds between the MM boundary atom and the MM atoms bonded to it; in the balanced redistributed charge-2 (BRC2) scheme, the adjusted MM boundary charge is distributed as point charges in equal portions to the MM atoms that are bonded to the MM boundary atom. The QM subsystem is capped by a fluorine atom that is tuned to reproduce the sum of partial atomic charges of the uncapped portion of the QM subsystem. The new aspect of the present study is a new way to carry out the tuning process; in particular, the CM5 charge model, rather than the Mulliken population analysis applied in previous studies, is used for tuning the capping atom that terminates the dangling bond of the QM region. The mean unsigned error (MUE) of the QM/MM deprotonation energy for a 15-system test suite of deprotonation reactions is 2.3 kcal/mol for the tuned BSRC scheme (TBSRC) and 2.4 kcal/mol for the tuned BRC2 scheme (TBRC2). As was the case for the original tuning method based on Mulliken charges, the new tuning method performs much better than using conventional hydrogen link atoms, which have an MUE on this test set of about 7 kcal/mol. However, the new scheme eliminates the need to use small basis sets, which can be problematic, and it allows one to be more consistent by tuning the parameters with whatever basis set is appropriate for applications. (Alternatively, since the tuning parameters and partial charges

13C and 1H nuclear magnetic resonance of methyl-substituted acetophenones and methyl benzoates: steric hindrance and inhibited conjugation.

Science.gov (United States)

Budesínský, Milos; Kulhánek, Jirí; Böhm, Stanislav; Cigler, Petr; Exner, Otto

2004-10-01

The 1H and 13C NMR spectra of 14 methyl-substituted acetophenones and 14 methyl-substituted methyl benzoates were assigned and interpreted with respect to the conformation of the C(ar)-C(O) bond. The substituent effects are proportional in the two series and can be divided into polar and steric: each has different effects on the 13C SCS of the individual atoms. In the case of C atoms C(O), C(1) and CH3(CO), the steric effects were quantitatively separated by comparing SCS in the ortho and para positions. The steric effects are proportional for the individual C atoms and also to steric effects estimated from other physical quantities. However, they do not depend simply on the angle of torsion phi of the functional group as anticipated hitherto. A better description distinguishes two classes of compounds: sterically not hindered or slightly hindered planar molecules and strongly sterically hindered, markedly non-planar. In order to confirm this reasoning without empirical correlations, the J(C,C) coupling constants were measured for three acetophenone derivatives labeled with 13C in the acetyl methyl group. The constants confirm unambiguously the conformation of 2-methylacetophenone; their zero values are in accord with the conformation of 2,6-dimethylacetophenone. The zero values in the unsubstituted acetophenone are at variance with previous erroneous report but all J(C,C) values are in accord with calculations at the B3LYP/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level. Copyright 2004 John Wiley & Sons, Ltd.

Peptide Probes Reveal a Hydrophobic Steric Ratchet in the Anthrax Toxin Protective Antigen Translocase.

Science.gov (United States)

Colby, Jennifer M; Krantz, Bryan A

2015-11-06

Anthrax toxin is a tripartite virulence factor produced by Bacillus anthracis during infection. Under acidic endosomal pH conditions, the toxin's protective antigen (PA) component forms a transmembrane channel in host cells. The PA channel then translocates its two enzyme components, lethal factor and edema factor, into the host cytosol under the proton motive force. Protein translocation under a proton motive force is catalyzed by a series of nonspecific polypeptide binding sites, called clamps. A 10-residue guest/host peptide model system, KKKKKXXSXX, was used to functionally probe polypeptide-clamp interactions within wild-type PA channels. The guest residues were Thr, Ala, Leu, Phe, Tyr, and Trp. In steady-state translocation experiments, the channel blocked most tightly with peptides that had increasing amounts of nonpolar surface area. Cooperative peptide binding was observed in the Trp-containing peptide sequence but not the other tested sequences. Trp substitutions into a flexible, uncharged linker between the lethal factor amino-terminal domain and diphtheria toxin A chain expedited translocation. Therefore, peptide-clamp sites in translocase channels can sense large steric features (like tryptophan) in peptides, and while these steric interactions may make a peptide translocate poorly, in the context of folded domains, they can make the protein translocate more rapidly presumably via a hydrophobic steric ratchet mechanism. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Uncertainties in Steric Sea Level Change Estimation During the Satellite Altimeter Era: Concepts and Practices

Science.gov (United States)

MacIntosh, C. R.; Merchant, C. J.; von Schuckmann, K.

2017-01-01

This article presents a review of current practice in estimating steric sea level change, focussed on the treatment of uncertainty. Steric sea level change is the contribution to the change in sea level arising from the dependence of density on temperature and salinity. It is a significant component of sea level rise and a reflection of changing ocean heat content. However, tracking these steric changes still remains a significant challenge for the scientific community. We review the importance of understanding the uncertainty in estimates of steric sea level change. Relevant concepts of uncertainty are discussed and illustrated with the example of observational uncertainty propagation from a single profile of temperature and salinity measurements to steric height. We summarise and discuss the recent literature on methodologies and techniques used to estimate steric sea level in the context of the treatment of uncertainty. Our conclusions are that progress in quantifying steric sea level uncertainty will benefit from: greater clarity and transparency in published discussions of uncertainty, including exploitation of international standards for quantifying and expressing uncertainty in measurement; and the development of community "recipes" for quantifying the error covariances in observations and from sparse sampling and for estimating and propagating uncertainty across spatio-temporal scales.

Estimation of the Young’s modulus of cellulose Iß by MM3 and quantum mechanics

Science.gov (United States)

Young’s modulus provides a measure of the resistance to deformation of an elastic material. In this study, modulus estimations for models of cellulose Iß relied on calculations performed with molecular mechanics (MM) and quantum mechanics (QM) programs. MM computations used the second generation emp...

Extraction of UO22+ by two highly sterically hindered (X1) (X2) PO(OH) extractants from an aqueous chloride phase

International Nuclear Information System (INIS)

Mason, G.W.; Lewey, S.M.; Gilles, D.M.; Peppard, D.F.

1978-01-01

The comparative extraction behaviour of tracer-level UO 2 2+ into benzene solutions of two highly sterically hindered extractants, di(2,6-di-iso-propylphenyl) phosphoric acid, HD(2,6-i-PPHI)P and di-tertiary-butyl phosphinic acid, H[Dt-BP], vs an aqueous 1.0 F (NaCl + HCl) phase was studied. The extraction of UO 2 2+ in both systems is directly second-power dependent upon extractant concentration and inversely second-power dependent upon hydrogen ion concentration, the stoichiometry of extraction being UOsub(2A) 2+ + 2(HY)sub(2O) = UO 2 (HY 2 )sub(2O) + 2Hsub(A) + . The expression for the distribution ratio, K is K = Ksub(s)F 2 /[H + ] 2 the general expression for the extraction of any metallic species being K - Ksub(s)Fsup(a)/[H + ]sup(b) where Ksub(s) is a constant characteristic of the system, F the concentration in formality units of extractant in the organic phase, [H + ] the concentration of hydrogen ion in the aqueous phase, and a and b the respective extractant and hydrogen-ion dependencies. Both extractants have a high degree of steric hindrance. The HD(2,6-i-PPHI)P is the more highly acidic, the pKsub(A) value, in 75% ethanol, being 3.2. The pKsub(A), previously reported, for H[Dt-BP] is 6.26. The Ksub(s) for UO 2 2+ in the system HY in benzene diluent vs an aqueous 1.0 F (NaCl + HCl) phase is 2 x 10 4 for H[Dt-BP] and 3 x 10 -1 for HD(2,6-i-PPHI)P; the ratio of the Ksub(s) values nearly 7 x 10 3 , favours the less acidic extractant. For comparative purposes, the Ksub(s) values for UO 2 2+ and for Am 3+ and Eu 3+ in other (X 1 )(X 2 )PO(OH), in benzene diluent, vs 1.0 F (NaCl + HCl) systems are presented. The variations are discussed in terms of the pKsub(A) of the extractant and the steric hindrance within the extractant. (author)

Sterically demanding diphosphonite ligands - synthesis and application in nickel-catalyzed isomerization of 2-methyl-3-butenenitrile

NARCIS (Netherlands)

Vlugt, van der J.I.; Hewat, A.C.; Neto, S.; Sablong, R.J.; Mills, A.M.; Lutz, M.; Spek, A.L.; Müller, C.; Vogt, D.

2004-01-01

The synthesis of a novel class of sterically demanding diphosphonites 1-8, based on rigid backbones, is described. The starting materials are all commercially available and the methodology allows for a modular approach. All ligands have been fully characterized, including an X-ray crystal structure

Optimal results of aortic valve replacement with small mechanical valves (< 19 mm).

Science.gov (United States)

Kato, Yasuyuki; Hattori, Koji; Motoki, Manabu; Takahashi, Yosuke; Kotani, Shinsuke; Nishimura, Shinsuke; Shibata, Toshihiko

2013-07-01

Controversy exists regarding the optimal operative method or type of prosthesis for patients with a small aortic root. The aim of this retrospective study was to investigate the early and mid-term outcomes of standard aortic valve replacement (AVR) using 16 mm or 18 mm ATS Advanced Performance (AP) or 17 mm St. Jude Medical (SJM) Regent valves for a small aortic root. Between April 2003 and August 2009, 78 patients (age range: 50-86 years; 86% aged > or = 65 years) underwent AVR with 16 mm or 18 mm ATS AP valves (16AP group: n = 21, 18AP group: n = 32), or a 17 mm SJM Regent valve (17Regent group: n = 25). Fifty-six patients (72%) had a body surface area (BSA) of regression was similar among the groups (-30%, -25% and -28% in the 16AP, 17Regent and 18AP groups, respectively; p = 0.844). The early and mid-term results of AVR with 16 mm or 18 mm ATS AP valves, or with a 17 mm SJM Regent valve, were satisfactory. Therefore, standard AVR using these small mechanical prostheses, which avoids the need to enlarge the annulus or to conduct stentless bioprosthesis implantation, might represent an acceptable method, especially in elderly patients with a small aortic root.

Steric sea level variability (1993-2010) in an ensemble of ocean reanalyses and objective analyses

Science.gov (United States)

Storto, Andrea; Masina, Simona; Balmaseda, Magdalena; Guinehut, Stéphanie; Xue, Yan; Szekely, Tanguy; Fukumori, Ichiro; Forget, Gael; Chang, You-Soon; Good, Simon A.; Köhl, Armin; Vernieres, Guillaume; Ferry, Nicolas; Peterson, K. Andrew; Behringer, David; Ishii, Masayoshi; Masuda, Shuhei; Fujii, Yosuke; Toyoda, Takahiro; Yin, Yonghong; Valdivieso, Maria; Barnier, Bernard; Boyer, Tim; Lee, Tony; Gourrion, Jérome; Wang, Ou; Heimback, Patrick; Rosati, Anthony; Kovach, Robin; Hernandez, Fabrice; Martin, Matthew J.; Kamachi, Masafumi; Kuragano, Tsurane; Mogensen, Kristian; Alves, Oscar; Haines, Keith; Wang, Xiaochun

2017-08-01

Quantifying the effect of the seawater density changes on sea level variability is of crucial importance for climate change studies, as the sea level cumulative rise can be regarded as both an important climate change indicator and a possible danger for human activities in coastal areas. In this work, as part of the Ocean Reanalysis Intercomparison Project, the global and regional steric sea level changes are estimated and compared from an ensemble of 16 ocean reanalyses and 4 objective analyses. These estimates are initially compared with a satellite-derived (altimetry minus gravimetry) dataset for a short period (2003-2010). The ensemble mean exhibits a significant high correlation at both global and regional scale, and the ensemble of ocean reanalyses outperforms that of objective analyses, in particular in the Southern Ocean. The reanalysis ensemble mean thus represents a valuable tool for further analyses, although large uncertainties remain for the inter-annual trends. Within the extended intercomparison period that spans the altimetry era (1993-2010), we find that the ensemble of reanalyses and objective analyses are in good agreement, and both detect a trend of the global steric sea level of 1.0 and 1.1 ± 0.05 mm/year, respectively. However, the spread among the products of the halosteric component trend exceeds the mean trend itself, questioning the reliability of its estimate. This is related to the scarcity of salinity observations before the Argo era. Furthermore, the impact of deep ocean layers is non-negligible on the steric sea level variability (22 and 12 % for the layers below 700 and 1500 m of depth, respectively), although the small deep ocean trends are not significant with respect to the products spread.

Histomorphological and immunofluorescence evaluation of clear corneal incisions after microcoaxial phacoemulsification with 2.2 mm and 1.8 mm systems.

Science.gov (United States)

Vasavada, Abhay R; Johar, Kaid; Praveen, Mamidipudi R; Vasavada, Viraj A; Arora, Anshul I

2013-04-01

To compare changes in the incision's histomorphology and denaturation of collagen I in rabbit eyes having microcoaxial phacoemulsification through 2.2 mm and 1.8 mm incision-compatible systems. Randomized experimental trial. Iladevi Cataract & IOL Research Centre, Ahmedabad, India. Thirty rabbit eyes were randomized into Group 1 (microcoaxial phacoemulsification through 2.2 mm incisions using Infiniti system [torsional ultrasound]) and Group 2 (microcoaxial phacoemulsification through 1.8 mm incisions using Stellaris system [longitudinal ultrasound]). Each group was then divided into 3 subgroups of 5 eyes each based on 1 of the 3 intervention options: phacoemulsification only, intraocular lens (IOL) insertion only, and phacoemulsification with IOL insertion. Left eyes were randomized for microcoaxial phacoemulsification, and right eyes were treated as controls. After phacoemulsification, eyes in Group 1 showed loss of epithelium at the roof of the incisions and Descemet membrane detachment at the floor of the incisions. These findings did not change after IOL insertion. After phacoemulsification, eyes in Group 2 showed loss of epithelium, but Descemet membrane remained attached. There was a longitudinal split in the incision's stroma in the direction of internal entry. The stromal damage increased after IOL implantation. Immunofluorescence studies showed no obvious irregularities in the arrangement of collagen I in either group. A dot blot analysis showed significant denaturation of collagen I in Group 2. The histomorphology of the 2.2 mm system incision showed localized Descemet membrane detachment and endothelial cell loss. The 1.8 mm system incision showed exaggerated stromal damage after IOL insertion. Copyright © 2013 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Steric Maps to Evaluate the Role of Steric Hindrance on the IPr NHC Ligand

KAUST Repository

Poater, Albert

2013-06-01

Density functional theory (DFT) calculations were used to predict and rationalize the effect of the modification of the structure of the prototype 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) (IPr) N-heterocyclic carbene (NHC) ligand. The modification consists in the substitution of the methyl groups of ortho isopropyl substituent with phenyl groups, and here we plan to describe how such significant changes effect the metal environment and therefore the related catalytic behaviour by simple steric maps. Bearing in mind that there is a significant structural difference between IPr and IPr* ligands, that translated in different reactivity for several olefin metathesis reactions, here by means of DFT we characterize where the NHC ligand plays a more active role and where it is a simple spectator, or at least its modification does not significantly change its catalytic role/performance. Furthermore, this communication endeavours to modify further the skeleton of the IPr NHC ligand. The optimization of these bulky new systems go to the limits of the DFT computational method.

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2.

Science.gov (United States)

Trnka, Tomáš; Kozmon, Stanislav; Tvaroška, Igor; Koča, Jaroslav

2015-04-01

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2.

Directory of Open Access Journals (Sweden)

Tomáš Trnka

2015-04-01

Full Text Available The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi. The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.

Steric and electronic parameters of a bulky yet flexible N-heterocyclic carbene: 1,3-bis(2,6-bis(1-ethylpropyl)phenyl)imidazol-2-ylidene (IPent)

KAUST Repository

Collado, Alba; Balogh, Já nos; Meiries, Sé bastien; Slawin, Alexandra M. Z.; Falivene, Laura; Cavallo, Luigi; Nolan, Steven P.

2013-01-01

The free N-heterocyclic carbene IPent (1; IPent = 1,3-bis(2,6-bis(1- ethylpropyl)phenyl)imidazol-2-ylidene) was prepared from the corresponding imidazolium chloride salt (2). The steric and electronic parameters of 1 were determined by synthesis of the gold(I) chloride complex [Au(IPent)Cl] (3) and the nickel-carbonyl complex [Ni(IPent)(CO)3] (4), respectively. 3 and 4 were fully characterized by NMR spectroscopy, elemental analysis, and X-ray diffraction studies on single crystals. © 2013 American Chemical Society.

Steric and electronic parameters of a bulky yet flexible N-heterocyclic carbene: 1,3-bis(2,6-bis(1-ethylpropyl)phenyl)imidazol-2-ylidene (IPent)

KAUST Repository

Collado, Alba

2013-06-10

The free N-heterocyclic carbene IPent (1; IPent = 1,3-bis(2,6-bis(1- ethylpropyl)phenyl)imidazol-2-ylidene) was prepared from the corresponding imidazolium chloride salt (2). The steric and electronic parameters of 1 were determined by synthesis of the gold(I) chloride complex [Au(IPent)Cl] (3) and the nickel-carbonyl complex [Ni(IPent)(CO)3] (4), respectively. 3 and 4 were fully characterized by NMR spectroscopy, elemental analysis, and X-ray diffraction studies on single crystals. © 2013 American Chemical Society.

In vitro circumvention of cisplatin resistance by the novel sterically hindered platinum complex AMD473.

Science.gov (United States)

Holford, J.; Sharp, S. Y.; Murrer, B. A.; Abrams, M.; Kelland, L. R.

1998-01-01

A novel sterically hindered platinum complex, AMD473 [cis-aminedichloro(2-methylpyridine) platinum (II)], has been selected for phase I clinical trials due to commence in 1997. AMD473 was rationally designed to react preferentially with nucleic acids over sulphur ligands such as glutathione. This report documents the in vitro circumvention of acquired cisplatin resistance mechanisms in human ovarian carcinoma (HOC) cell lines by AMD473. In a panel of 11 HOC cell lines, AMD473 showed intermediate growth inhibition potency (mean IC50 of 8.1 microM) in comparison to cisplatin (mean IC50 of 2.6 microM) and carboplatin (mean IC50 of 20.3 microM). AMD473 showed only a 30.7-fold increase in IC50 value from the most sensitive to the most resistant HOC cell line, whereas for cisplatin it was 117.9-fold and for carboplatin 119.7-fold. AMD473 also showed significantly (P or = 14 h for AMD473) after equitoxic doses were exposed to HOC cells for 2 h. AMD473 ICLs in the CH1 HOC cell line were slowly formed and showed no visible signs of being repaired 24 h after removal of drug. This was paralleled by a slower, longer lasting induction of p53 protein by equitoxic doses of AMD473 in HOC cell lines with wild-type p53. This new class of sterically hindered platinum compound, selected for clinical trial in 1997, may therefore elicit improved clinical response in intrinsically and acquired cisplatin-resistant tumours in the clinic. Images Figure 9 PMID:9472630

Effects of the steric hindrance of micropores in the hyper-cross-linked polymeric adsorbent on the adsorption of p-nitroaniline in aqueous solution

International Nuclear Information System (INIS)

Xiao, Guqing; Wen, Ruimin; Wei, Dongmei; Wu, Dan

2014-01-01

Graphical abstract: The hyper-cross-linked polymeric adsorbents (GQ-05 and GQ-03) with different steric hindrance of micropores were designed. The adsorption capacity and adsorption rate of PNA onto the two adsorbents followed the order GQ-05 > GQ-03. The steric hindrance of micropores was a crucial factor for the adsorption capacity and adsorption rate order. - Highlights: • Two adsorbents with different steric hindrance of micropores were designed. • The adsorption capacity and adsorption rate followed the order GQ-05 > GQ-03. • The steric hindrance of micropores was a crucial factor for the order. - Abstract: A hyper-cross-linked polymeric adsorbent with “-CH 2 -phenol-CH 2 -” as the cross-linked bridge (denoted GQ-05), and another hyper-cross-linked polymeric adsorbent with “-CH 2 -p-cresol-CH 2 -” as the cross-linked bridge (denoted GQ-03) were synthesized to reveal the effect of the steric hindrance of micropores in the hyper-cross-linked polymeric adsorbent on adsorption capacity and adsorption rate of p-nitroaniline (PNA) from aqueous solution. The results of adsorption kinetics indicated the order of the adsorption rate GQ-05 > GQ-03. The pseudo-first-order rate equation could describe the entire adsorption process of PNA onto GQ-05 while the equation characterized the adsorption process of GQ-03 in two stages. The order of the adsorption capacity GQ-05 > GQ-03 was demonstrated by thermodynamic analysis and dynamic adsorption. The steric hindrance of micropores in the hyper-cross-linked polymeric adsorbent was a crucial factor for the order of the adsorption capacity and adsorption rate

Estimating the magnitude of steric effects in rigid systems by NMR

International Nuclear Information System (INIS)

Yoneda, Julliane Diniz; Seidl, Peter Rudolf; Leal, Katia Zaccur

2008-01-01

The rapid advance of supramolecular chemistry has led to a better understanding of the forces and interactions that are responsible for many different phenomena. Among these, steric effects play an important role in determining the constraints to association between the species involved. Although the role of steric effects has been recognized for a long time, quantitative information has been mainly related to the comparison of these effects on a chemical reaction or conformational equilibrium rather than the properties of the group of atoms that is responsible for their manifestation. This situation has been changing with the increase in power of computational methods and the accumulation of data on model compounds that can be used for the purpose of comparison. Here we present a short review of our recent work on NMR of rigid carbocyclic systems and apply this type of approach to di- and triamantane systems. Our results show how NMR can be used to locate the segment of a molecule that is subjected to steric effects and evaluate the degree to which these effects will distort its geometry. (author)

Estimating the magnitude of steric effects in rigid systems by NMR

Energy Technology Data Exchange (ETDEWEB)

Yoneda, Julliane Diniz [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Programa Pos-Graduacao em Quimica Organica; Seidl, Peter Rudolf [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola de Quimica; Leal, Katia Zaccur, E-mail: pseidl@eq.ufrj.br [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Fisico-Quimica. Programa de Pos-Graduacao em Quimica Organica

2008-07-01

The rapid advance of supramolecular chemistry has led to a better understanding of the forces and interactions that are responsible for many different phenomena. Among these, steric effects play an important role in determining the constraints to association between the species involved. Although the role of steric effects has been recognized for a long time, quantitative information has been mainly related to the comparison of these effects on a chemical reaction or conformational equilibrium rather than the properties of the group of atoms that is responsible for their manifestation. This situation has been changing with the increase in power of computational methods and the accumulation of data on model compounds that can be used for the purpose of comparison. Here we present a short review of our recent work on NMR of rigid carbocyclic systems and apply this type of approach to di- and triamantane systems. Our results show how NMR can be used to locate the segment of a molecule that is subjected to steric effects and evaluate the degree to which these effects will distort its geometry. (author)

Chemical mechanical polisher technology for 300mm/0.18-0.13{mu}m semiconductor devices; 300mm/0.18-0.-0.13{mu}m sedai no CMP gijutsu

Energy Technology Data Exchange (ETDEWEB)

Tsujimura, M.; Kobayashi, F. [Ebara Corp., Tokyo (Japan)

1998-10-20

Described herein are problems involved in, and development points and measures for chemical mechanical polisher (CMP) technology for the generation of 300mm/0.18 to 0.13{mu}m semiconductor devices. Ebara has developed a CMP system for 300mm devices for I300I and Selete (semiconductor high-technologies). The polishing process conditions are set for the time being based on those for the 200mm devices, and the driver and machine structures are set at 2.25 times larger than those for the 200mm devices. Its space requirement is compacter at 1.3 times increase. The company has adopted a concept of `dry-in and dry-out,` which is not common for a CMP. This needs integration of the washer with the polisher, and aerodynamic designs for dust-free conditions. These are already developed for the 200mm devices, and applicable to the 300mm devices without causing any problem. The special chamber for the conventional CMP can be dispensed with, reducing cost. Expendables, such as slurry pad, are being developed to double their service lives and halve their consumption. 8 figs.

3rd IEEE/IFToMM International Conference on Reconfigurable Mechanisms and Robots

CERN Document Server

Kong, Xianwen; Dai, Jian; ReMAR 2015; Advances in Reconfigurable Mechanisms and Robots II

2016-01-01

This book presents the most recent advances in the research and applications of reconfigurable mechanisms and robots. It collects 93 independently reviewed papers presented at the Third ASME/IFToMM International Conference on Reconfigurable Mechanisms and Robots (ReMAR 2015) held in Beijing, China, 20-22 July 2015. The conference papers are organized into seven parts to cover the reconfiguration theory, topology, kinematics and design of reconfigurable mechanisms including reconfigurable parallel mechanisms. The most recent results on reconfigurable robots are presented including their analysis, design, simulation and control. Bio-inspired mechanisms are also explored in the challenging fields of rehabilitation and minimally invasive surgery. This book further addresses deployable mechanisms and origami-inspired mechanisms and showcases a wide range of successful applications of reconfigurable mechanisms and robots. Advances in Reconfigurable Mechanisms and Robots II should be of interest for researchers, eng...

5th IFToMM Symposium on the History of Machines and Mechanisms

CERN Document Server

Ceccarelli, Marco

2016-01-01

This volume includes contributions presented at the Fifth IFToMM Symposium on the History of Machines and Mechanisms, held at Universidad Autonoma de Queretaro, Santiago de Queretaro, QRO, Mexico, in June 2016. It contains work on theories and facts concerning mechanisms and machines from antiquity to current times as viewed in the present day. Topics include modern reviews of past works; people, history, and their works; direct memories of the recent past; historic development theories; the history of the design of machines and mechanisms; developments of mechanical design and automation; the historic development of teaching; the history of schools of engineering and the education of engineers. .

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

Science.gov (United States)

Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

2012-01-01

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

A Molecular Dynamics (MD and Quantum Mechanics/Molecular Mechanics (QM/MM Study on Ornithine Cyclodeaminase (OCD: A Tale of Two Iminiums

Directory of Open Access Journals (Sweden)

James W. Gauld

2012-10-01

Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

2-mm microwave interferometer

International Nuclear Information System (INIS)

Futch, A.H.; Mortensen, W.K.

1977-01-01

A 2-mm microwave interferometer has been developed, and phase shift measurements have been made on the Baseball II experiment. The interferometer system employs a 140-GHz receiver for double down conversion of the plasma signal to a 60-MHz, IF frequency. The 140-GHz references signal is also down-converted and compared with the plasma signal to provide the desired phase change of the signal passing through the plasma. A feedback voltage from a 60-MHz discriminator to a voltage-controlled oscillator in the receiver provides frequency stability of the 60-MHz IF signals

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

Science.gov (United States)

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion.

Science.gov (United States)

Goodman, Lionel; Gu, Hongbing; Pophristic, Vojislava

2005-02-17

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.

Steric Pressure among Membrane-Bound Polymers Opposes Lipid Phase Separation.

Science.gov (United States)

Imam, Zachary I; Kenyon, Laura E; Carrillo, Adelita; Espinoza, Isai; Nagib, Fatema; Stachowiak, Jeanne C

2016-04-19

Lipid rafts are thought to be key organizers of membrane-protein complexes in cells. Many proteins that interact with rafts have bulky polymeric components such as intrinsically disordered protein domains and polysaccharide chains. Therefore, understanding the interaction between membrane domains and membrane-bound polymers provides insights into the roles rafts play in cells. Multiple studies have demonstrated that high concentrations of membrane-bound polymeric domains create significant lateral steric pressure at membrane surfaces. Furthermore, our recent work has shown that lateral steric pressure at membrane surfaces opposes the assembly of membrane domains. Building on these findings, here we report that membrane-bound polymers are potent suppressors of membrane phase separation, which can destabilize lipid domains with substantially greater efficiency than globular domains such as membrane-bound proteins. Specifically, we created giant vesicles with a ternary lipid composition, which separated into coexisting liquid ordered and disordered phases. Lipids with saturated tails and poly(ethylene glycol) (PEG) chains conjugated to their head groups were included at increasing molar concentrations. When these lipids were sparse on the membrane surface they partitioned to the liquid ordered phase. However, as they became more concentrated, the fraction of GUVs that were phase-separated decreased dramatically, ultimately yielding a population of homogeneous membrane vesicles. Experiments and physical modeling using compositions of increasing PEG molecular weight and lipid miscibility phase transition temperature demonstrate that longer polymers are the most efficient suppressors of membrane phase separation when the energetic barrier to lipid mixing is low. In contrast, as the miscibility transition temperature increases, longer polymers are more readily driven out of domains by the increased steric pressure. Therefore, the concentration of shorter polymers required

Steric parameters and excess properties of hydroxamic acids

International Nuclear Information System (INIS)

Patre, Sandhya; Thakur, Piyush; Pande, Rama

2012-01-01

Graphical abstract: Plot of excess molar volume, V E , vs X 2 of (A) PBHA in DMF, (B) PMNHA in DMF, and (C) PNHA in DMF, at (■), 298.15 K; (▪), 303.15 K; (▪), 308.15 K; and (▪), 313.15 K. Highlights: ► Apparent molar volume indicates greater solute–solvent interactions. ► Excess properties show higher dispersion force in solution than pure solvent. ► Excess parameters suggest strong solute–solvent and solute–solute interactions. ► Limiting apparent molar expansibilities instigate highly hydrophobic characters. ► Hepler’s constant suggest the structure promoter nature of hydroxamic acids. - Abstract: Steric parameters of N-phenylbenzo-, N-phenyl-4-methyl-3-nitrobenzo-, and N-phenyl-4-nitrobenzo-, hydroxamic acids were measured in N,N-dimethylformamide (DMF) as a function of their concentrations at T = (298.15, 303.15, 308.15, and 313.15) K. The apparent molar volume (V φ ), limiting apparent molar volume (V φ 0 ) at infinite dilution and the slope (S V ∗ ) are calculated from the experimental values of density (ρ) by applying the Masson’s equation. The apparent molar expansibility at infinite dilution (φ E 0 ), molar volume (V) and the excess molar volume (V E ) are also computed. The refractive indices (n) have been used to calculate the steric parameters, viz. molar refraction (R M ), polarizability (α) and excess molar refraction (R) of these molecules. The results show the strong solute–solvent interactions present in the system and thus, help to explore the molecular structure.

Parameterization of phosphine ligands demonstrates enhancement of nickel catalysis via remote steric effects

Science.gov (United States)

Wu, Kevin; Doyle, Abigail G.

2017-08-01

The field of Ni-catalysed cross-coupling has seen rapid recent growth because of the low cost of Ni, its earth abundance, and its ability to promote unique cross-coupling reactions. Whereas advances in the related field of Pd-catalysed cross-coupling have been driven by ligand design, the development of ligands specifically for Ni has received minimal attention. Here, we disclose a class of phosphines that enable the Ni-catalysed Csp3 Suzuki coupling of acetals with boronic acids to generate benzylic ethers, a reaction that failed with known ligands for Ni and designer phosphines for Pd. Using parameters to quantify phosphine steric and electronic properties together with regression statistical analysis, we identify a model for ligand success. The study suggests that effective phosphines feature remote steric hindrance, a concept that could guide future ligand design tailored to Ni. Our analysis also reveals that two classic descriptors for ligand steric environment—cone angle and % buried volume—are not equivalent, despite their treatment in the literature.

Abstraction of iodine from aromatic iodides by alkyl radicals: steric and electronic effects.

Science.gov (United States)

Dolenc, Darko; Plesnicar, Bozo

2006-10-13

Abstraction of the iodine atom from aryl iodides by alkyl radicals takes place in some cases very efficiently despite the unfavorable difference in bond dissociation energies of C-I bonds in alkyl and aryl iodides. The abstraction is most efficient in iodobenzenes, ortho-substituted with bulky groups. The ease of abstraction can be explained by the release of steric strain during the elimination of the iodine atom. The rate of abstraction correlates fairly well with the strain energy, calculated by density functional theory (DFT) and Hartree-Fock (HF) methods as a difference in the total energy of ortho and para isomers. However, besides the steric bulk, the presence of some other functional groups in an ortho substituent also influences the rate. The stabilization of the transition state, resembling a 9-I-2 iodanyl radical, by electron-withdrawing groups seems to explain a positive sign of the Hammett rho value in the radical abstraction of halogen atoms.

Magnetic and mechanical design of a 130 mm aperture Nb{sub 3}Sn dipole magnet

Energy Technology Data Exchange (ETDEWEB)

Felice, H.; Vedrine, P. [CEA Saclay, DAPNIA/SACM/LEAS, F-91191 Gif Sur Yvette, (France); Mailfert, A. [LEM, F-54500 Vandoeuvre Les Nancy, (France)

2007-07-01

For the next generation of dipoles for accelerators, two main challenges come into play. In one hand, high dipolar fields in the range of 13 to 15 T are targeted. In the other hand, large apertures (above 80 mm) are required in the interaction regions. These two requirements lead to two issues. First, a new superconductor has to replace the NbTi as its limits have been reached around 10 T with the LHC. The superconducting material liable to be its successor is the Nb{sub 3}Sn. However, it is a very mechanical stress sensitive material. Up to now, a mechanical stress of 150 MPa is supposed to degrade its critical properties. Second, large aperture dipole can not be considered with the well-known cosine theta design. Indeed, above 88 mm, azimuthal Lorentz forces in this magnetic configuration produces mechanical stresses on the coil midplane higher than the acceptable limit. In this paper, an alternative coil arrangement based on intersecting ellipses and limiting the mechanical stresses is proposed for a 130 mm aperture dipole. The first part of this paper is dedicated to the magnetic study of this magnet. We can underline the fact that the field quality required in particle accelerators can be reached with a bore field of about 13 T. The second part deals with the mechanical structure of the magnet which is necessary to withstand the Lorentz forces involved and to apply pre-stress. (authors)

Steric and Stereochemical Modulation in Pyridyl- and Quinolyl-Containing Ligands

Directory of Open Access Journals (Sweden)

Zhaohua Dai

2016-12-01

Full Text Available Nitrogen-containing pyridine and quinoline are outstanding platforms on which excellent ionophores and sensors for metal ions can be built. Steric and stereochemical effects can be used to modulate the affinity and selectivity of such ligands toward different metal ions on the coordination chemistry front. On the signal transduction front, such effects can also be used to modulate optical responses of these ligands in metal sensing systems. In this review, steric modulation of achiral ligands and stereochemical modulation in chiral ligands, especially ionophores and sensors for zinc, copper, silver, and mercury, are examined using published structural and spectral data. Although it might be more challenging to construct chiral ligands than achiral ones, isotropic and anisotropic absorption signals from a single chiroptical fluorescent sensor provide not only detection but also differentiation of multiple analytes with high selectivity.

Mercury(II) and methylmercury(II) complexes of novel sterically hindered thiolates: 13C and 199Hg NMR studies and the crystal and molecular structures of [MeHg(SC6H2-2,4,6-Pri3)], [Hg(SC6H4-2-SiMe3)2], [Hg(2-SC5H3N-3-SiMe3)2], and [Hg{(2-SC6H4)2SiMe2}]2

International Nuclear Information System (INIS)

Block, E.; Brito, M.; Gernon, M.; McGowty, D.; Kang, Hyunkyu; Zubieta, J.

1990-01-01

Several series of complexes of the types [MeHg(SR)] and [Hg(SR) 2 ] have been synthesized, where the ligands are members of new classes of sterically hindered thiolates, including (triorganosilyl)methanethiols, 2-(triorganosilyl)benzenethiols, 3-(triorganosilyl)pyridine-2-thiols, and bis(2-mercaptophenyl) derivatives. Detailed 1 H, 13 C, and 199 Hg NMR studies revealed several general trends. The 199 Hg chemical shifts moved upfield in the order [MeHg(SR)] 2 ] 2 ] 2 ]. For the [MeHg(SR)] series of complexes, 1 J(Hg-C) correlates with δ( 13 C(methyl)) and with the type of thiolate ligand. Anomalous behavior is observed for oligomeric species. There is only a limited correlation of δ( 199 Hg) with steric cone angles for a subset of the complexes. Crystal data for the complexes are reported. 86 refs., 7 figs., 11 tabs

A QM/MM study of the catalytic mechanism of nicotinamidase.

Science.gov (United States)

Sheng, Xiang; Liu, Yongjun

2014-02-28

Nicotinamidase (Pnc1) is a member of Zn-dependent amidohydrolases that hydrolyzes nicotinamide (NAM) to nicotinic acid (NA), which is a key step in the salvage pathway of NAD(+) biosynthesis. In this paper, the catalytic mechanism of Pnc1 has been investigated by using a combined quantum-mechanical/molecular-mechanical (QM/MM) approach based on the recently obtained crystal structure of Pnc1. The reaction pathway, the detail of each elementary step, the energetics of the whole catalytic cycle, and the roles of key residues and Zn-binding site are illuminated. Our calculation results indicate that the catalytic water molecule comes from the bulk solvent, which is then deprotonated by residue D8. D8 functions as a proton transfer station between C167 and NAM, while the activated C167 serves as the nucleophile. The residue K122 only plays a role in stabilizing intermediates and transition states. The oxyanion hole formed by the amide backbone nitrogen atoms of A163 and C167 has the function to stabilize the hydroxyl anion of nicotinamide. The Zn-binding site rather than a single Zn(2+) ion acts as a Lewis acid to influence the reaction. Two elementary steps, the activation of C167 in the deamination process and the decomposition of catalytic water in the hydrolysis process, correspond to the large energy barriers of 25.7 and 28.1 kcal mol(-1), respectively, meaning that both of them contribute a lot to the overall reaction barrier. Our results may provide useful information for the design of novel and efficient Pnc1 inhibitors and related biocatalytic applications.

A comparable study of clinical and optical outcomes after 1.8, 2.0 mm microcoaxial and 3.0 mm coaxial cataract surgery.

Science.gov (United States)

Yu, Yi-Bo; Zhu, Ya-Nan; Wang, Wei; Zhang, Yi-Dong; Yu, Yin-Hui; Yao, Ke

2016-01-01

To evaluate the clinical and optical outcomes after clear corneal incision cataract surgery (CICS) with three different incision sizes (1.8, 2.0 and 3.0 mm). Eyes of 150 patients with age-related cataract scheduled for coaxial cataract surgery were randomized to three groups: 1.8, 2.0, or 3.0 mm CICS. Intraoperative data and postoperative outcomes including surgically induced astigmatism (SIA), the corneal incision thickness, wavefront aberrations and modulation transfer function (MTF) of cornea were obtained. There were no significant differences among the three groups in demographic characteristics and intraoperative outcome. The 1.8 and 2.0 mm microincisions showed more satisfactory clinical outcomes than the 3.0 mm incision. The 1.8 mm incision showed significantly less SIA than the 2.0 mm incision until postoperative 1mo (P0.05). Converting from 3.0 mm CICS to 1.8 or 2.0 mm CICS result in better clinical and optical outcomes. However, when incision is 1.8 mm, the benefits from further reduction in size compared with 2.0 mm are limited. The necessity to reduce the incision size is to be deliberated.

Semiconducting perovskites (2-XC6H4C2H4NH3)2SnI4 (X = F, Cl, Br): steric interaction between the organic and inorganic layers.

Science.gov (United States)

Xu, Zhengtao; Mitzi, David B; Dimitrakopoulos, Christos D; Maxcy, Karen R

2003-03-24

Two new semiconducting hybrid perovskites based on 2-substituted phenethylammonium cations, (2-XC(6)H(4)C(2)H(4)NH(3))(2)SnI(4) (X = Br, Cl), are characterized and compared with the previously reported X = F compound, with a focus on the steric interaction between the organic and inorganic components. The crystal structure of (2-ClC(6)H(4)C(2)H(4)NH(3))(2)SnI(4) is solved in a disordered subcell [C2/m, a = 33.781(7) A, b = 6.178(1) A, c = 6.190(1) A, beta = 90.42(3)(o), and Z = 2]. The structure is similar to the known (2-FC(6)H(4)C(2)H(4)NH(3))(2)SnI(4) structure with regard to both the conformation of the organic cations and the bonding features of the inorganic sheet. The (2-BrC(6)H(4)C(2)H(4)NH(3))(2)SnI(4) system adopts a fully ordered monoclinic cell [P2(1)/c, a = 18.540(2) A, b = 8.3443(7) A, c = 8.7795(7) A, beta = 93.039(1)(o), and Z = 2]. The organic cation adopts the anti conformation, instead of the gauche conformation observed in the X = F and Cl compounds, apparently because of the need to accommodate the additional volume of the bromo group. The steric effect of the bromo group also impacts the perovskite sheet, causing notable distortions, such as a compressed Sn-I-Sn bond angle (148.7(o), as compared with the average values of 153.3 and 154.8(o) for the fluoro and chloro compounds, respectively). The optical absorption features a substantial blue shift (lowest exciton peak: 557 nm, 2.23 eV) relative to the spectra of the fluoro and chloro compounds (588 and 586 nm, respectively). Also presented are transport properties for thin-film field-effect transistors (TFTs) based on spin-coated films of the two hybrid semiconductors.

Mechanical properties and microstructural investigations of TIG welded 40 mm and 60 mm thick SS 316L samples for fusion reactor vacuum vessel applications

Energy Technology Data Exchange (ETDEWEB)

Buddu, Ramesh Kumar, E-mail: brkumar75@gmail.com; Chauhan, N.; Raole, P.M.

2014-12-15

Highlights: • Austenitic stainless steels (316L) of 40 mm and 60 mm thickness plates were joined by Tungsten Inert Gas welding (TIG) process which are probable materials for advanced fusion reactor vacuum vessel requirements. • Mechanical properties and detailed microstructure studies have been carried out for welded samples. • Fractography analysis of impact test specimens indicated ductile fracture mode in BM, HAZ and WZ samples. • Presence of delta ferrite phase was observed in the welded zone and ferrite number data was measured for the base and weld metal and was found high in welds. - Abstract: The development of advanced fusion reactors like DEMO will have various challenges in materials and fabrication. The vacuum vessel is important part of the fusion reactor. The double walled design for vacuum vessel with thicker stainless steel material (40–60 mm) has been proposed in the advanced fusion reactors like ITER. Different welding techniques will have to be used for such vacuum vessel development. The required mechanical, structural and other properties of stainless steels have to be maintained in these joining processes of components of various shapes and sizes in the form of plates, ribs, shells, etc. The present paper reports characterization of welding joints of SS316L plates with higher thicknesses like 40 mm and 60 mm, prepared using multi-pass Tungsten Inert Gas (TIG) welding process. The weld quality has been evaluated with non-destructive tests by X-ray radiography and ultrasonic methods. The mechanical properties like tensile, bend tests, Vickers hardness and impact fracture tests have been carried out for the weld samples. Tensile property test results indicate sound weld joints with efficiencies over 100%. Hardening was observed in the weld zone in non-uniform manner. Macro and microstructure studies have been carried out for Base Metal (BM), Heat Affected Zone (HAZ) and Weld Zone (WZ). Scanning Electron Microscopy (SEM) analysis carried

Mechanical properties and microstructural investigations of TIG welded 40 mm and 60 mm thick SS 316L samples for fusion reactor vacuum vessel applications

International Nuclear Information System (INIS)

Buddu, Ramesh Kumar; Chauhan, N.; Raole, P.M.

2014-01-01

Highlights: • Austenitic stainless steels (316L) of 40 mm and 60 mm thickness plates were joined by Tungsten Inert Gas welding (TIG) process which are probable materials for advanced fusion reactor vacuum vessel requirements. • Mechanical properties and detailed microstructure studies have been carried out for welded samples. • Fractography analysis of impact test specimens indicated ductile fracture mode in BM, HAZ and WZ samples. • Presence of delta ferrite phase was observed in the welded zone and ferrite number data was measured for the base and weld metal and was found high in welds. - Abstract: The development of advanced fusion reactors like DEMO will have various challenges in materials and fabrication. The vacuum vessel is important part of the fusion reactor. The double walled design for vacuum vessel with thicker stainless steel material (40–60 mm) has been proposed in the advanced fusion reactors like ITER. Different welding techniques will have to be used for such vacuum vessel development. The required mechanical, structural and other properties of stainless steels have to be maintained in these joining processes of components of various shapes and sizes in the form of plates, ribs, shells, etc. The present paper reports characterization of welding joints of SS316L plates with higher thicknesses like 40 mm and 60 mm, prepared using multi-pass Tungsten Inert Gas (TIG) welding process. The weld quality has been evaluated with non-destructive tests by X-ray radiography and ultrasonic methods. The mechanical properties like tensile, bend tests, Vickers hardness and impact fracture tests have been carried out for the weld samples. Tensile property test results indicate sound weld joints with efficiencies over 100%. Hardening was observed in the weld zone in non-uniform manner. Macro and microstructure studies have been carried out for Base Metal (BM), Heat Affected Zone (HAZ) and Weld Zone (WZ). Scanning Electron Microscopy (SEM) analysis carried

Revealing climate modes in steric sea levels: lessons learned from satellite geodesy, objective analyses and ocean reanalyses

Science.gov (United States)

Pfeffer, J.; Tregoning, P.; Purcell, A. P.

2017-12-01

Due to increased greenhouse gases emissions, the oceans are accumulating heat. In response to the ocean circulation and atmospheric forcing, the heat is irregularly redistributed within the oceans, causing sea level to rise at variable rates in space and time. These rates of steric expansion are extremely difficult to assess because of the sparsity of in-situ hydrographic observations available within the course of the 20th century. We compare here three methods to reconstruct the steric sea levels over the past 13, 25 and 58 years based on satellite geodesy, objective analyses and ocean reanalyses. The interannual to decadal variability of each dataset is explored with a model merging six climate indices representative of the natural variability of the ocean and climate system. Consistent regional patterns are identified for the Pacific Decadal Oscillation (PDO) and El Niño Southern Oscillation (ENSO) in all datasets at all timescales. Despite the short time coverage (13 years), the combination of satellite geodetic data (altimetry and GRACE) also reveals significant steric responses to the North Pacific Gyre Oscillation (NPGO), Indian Dipole (IOD) and Indian ocean basinwide (IOBM) mode. The richer information content in the ocean reanalyses allows us to recover the regional fingerprints of the PDO, ENSO, NPGO, IOD and IOBM, but also of the Atlantic Multidecadal Oscillation (AMO) acting over longer time scales (40 to 60 years). Therefore, ocean reanalyses, coupled with climate mode analyses, constitute innovative and promising tools to investigate the mechanisms triggering the variability of sea level rise over the past decades.

Influence of Striking Edge Radius (2 mm versus 8 mm) on Instrumented Charpy Data and Absorbed Energies

Energy Technology Data Exchange (ETDEWEB)

Lucon, E.

2008-08-15

The most commonly used test standards for performing Charpy impact tests (ISO 148 and ASTM E 23) envisage the use of strikers having different radii of the striking edge, i.e. 2 mm (ISO) and 8 mm (ASTM). The effect of striker geometry on Charpy results was extensively studied in the past in terms of absorbed energy measured by the machine encoder, but few investigations are available on the influence of striker configuration on the results of instrumented Charpy tests (characteristic forces, displacements and integrated energy). In this paper, these effects are investigated based on the analysis of published results from three interlaboratory studies and some unpublished Charpy data obtained at SCK-CEN. The instrumented variables which are the most sensitive to the radius of the striking edge are the maximum force and its corresponding displacement, with 8mm-strikers providing systematically higher values. Absorbed energies, obtained both from the instrumented trace and from the pendulum encoder, are almost insensitive to the type of striker up to 200 J. For higher energy levels, the values obtained from 8mm strikers become progressively larger. Data scatter is generally higher for 2mm-strikers.

A protocol for amide bond formation with electron deficient amines and sterically hindered substrates

DEFF Research Database (Denmark)

Due-Hansen, Maria E; Pandey, Sunil K; Christiansen, Elisabeth

2016-01-01

A protocol for amide coupling by in situ formation of acyl fluorides and reaction with amines at elevated temperature has been developed and found to be efficient for coupling of sterically hindered substrates and electron deficient amines where standard methods failed.......A protocol for amide coupling by in situ formation of acyl fluorides and reaction with amines at elevated temperature has been developed and found to be efficient for coupling of sterically hindered substrates and electron deficient amines where standard methods failed....

Charpy impact test results on five materials and NIST verification specimens using instrumented 2-mm and 8-mm strikers

International Nuclear Information System (INIS)

Nanstad, R.K.; Sokolov, M.A.

1995-01-01

The Heavy-Section Steel Irradiation Program at Oak Ridge National Laboratory is involved in two cooperative projects, with international participants, both of which involve Charpy V-notch impact tests with instrumented strikers of 2mm and 8mm radii. Two heats of A 533 grade B class I pressure vessel steel and a low upper-shelf (LUS) submerged-arc (SA) weld were tested on the same Charpy machine, while one heat of a Russian Cr-Mo-V forging steel and a high upper-shelf (HUS) SA weld were tested on two different machines. The number of replicate tests at any one temperature ranged from 2 to 46 specimens. Prior to testing with each striker, verification specimens at the low, high, and super high energy levels from the National Institute of Standards and Technology (NIST) were tested. In the two series of verification tests, the tests with the 2mm striker met the requirements at the low and high energy levels but not at the super high energy. For one plate, the 2mm striker showed somewhat higher average absorbed energies than those for the 8-mm striker at all three test temperatures. For the second plate and the LUS weld, however, the 2mm striker showed somewhat lower energies at both test temperatures. For the Russian forging steel and the HUS weld, tests were conducted over a range of temperatures with tests at one laboratory using the 8mm striker and tests at a second laboratory using the 2mm striker. Lateral expansion was measured for all specimens and the results are compared with the absorbed energy results. The overall results showed generally good agreement (within one standard deviation) in energy measurements by the two strikers. Load-time traces from the instrumented strikers were also compared and used to estimate shear fracture percentage. Four different formulas from the European Structural Integrity Society draft standard for instrumented Charpy test are compared and a new formula is proposed for estimation of percent shear from the force-time trace

Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations.

Science.gov (United States)

Krámos, Balázs; Menyhárd, Dóra K; Oláh, Julianna

2012-01-19

Nitric oxide reductase (P450(nor)) found in Fusarium oxysporum catalyzes the reduction of nitric oxide to N(2)O in a multistep process. The reducing agent, NADH, is bound in the distal pocket of the enzyme, and direct hydride transfer occurs from NADH to the nitric oxide bound heme enzyme, forming intermediate I. Here we studied the possibility of hydride transfer from NADH to both the nitrogen and oxygen of the heme-bound nitric oxide, using quantum chemical and combined quantum mechanics/molecular mechanics (QM/MM) calculations, on two different protein models, representing both possible stereochemistries, a syn- and an anti-NADH arrangement. All calculations clearly favor hydride transfer to the nitrogen of nitric oxide, and the QM-only barrier and kinetic isotope effects are good agreement with the experimental values of intermediate I formation. We obtained higher barriers in the QM/MM calculations for both pathways, but hydride transfer to the nitrogen of nitric oxide is still clearly favored. The barriers obtained for the syn, Pro-R conformation of NADH are lower and show significantly less variation than the barriers obtained in the case of anti conformation. The effect of basis set and wide range of functionals on the obtained results are also discussed.

Composite outcomes in 2.25-mm drug eluting stents: a systematic review

International Nuclear Information System (INIS)

Lee, Justin Z.; Singh, Nirmal; Ortega, Gilbert; Low, See Wei; Kanakadandi, Uday; Fortuin, F. David; Lassar, Tom; Lee, Kwan S.

2015-01-01

Background: Coronary atherosclerosis often involves small-caliber coronaries, yet the safety and efficacy of 2.25-mm DES have been poorly defined, with a general lack of separation of 2.25 with 2.5-mm performance. No randomized head-to-head 2.25 mm DES studies have been reported. There are several single-arm prospective studies, and we aim to systematically review all published specific 2.25-mm data to estimate composite DES-specific performance and highlight current knowledge gaps. Methods: We performed a systematic literature search of PubMed, EMBASE, Web of Science and Cochrane database for clinical trials of 2.25-mm DES. Angiographic and composite clinical outcomes were compared with descriptive statistics. Results: 2.25 mm-Paclitaxel (PES), sirolimus (SES), everolimus (EES) and platinum chromium EES DES-specific outcomes have been reported. Death at 12 months for SES, PES, EES and platinum chromium EES was 1.3%, 3.0%, 1.5%, and 4.4%. Rates of target vessel revascularization at 12 months for SES, PES, EES and platinum chromium EES were 5.7%, 13.3%, 8.8%, and 3.3%. Angiographic outcomes at 9 months to one year were as follows: mean late lumen loss (LLL) for SES, PES, and EES was 0.15 ± 0.11-mm, 0.28 ± 0.11-mm, and 0.16 ± 0.41-mm and mean diameter restenosis for SES, PES, and EES were 29.5 ± 6.2%, 34.7 ± 4.2%, and 20.9 ± 22.5%. Reported stent thrombosis rates for 2.25-mm DES were low ranging from 0% to 2.2% in up to 24-months of follow-up. Conclusions: This systematic review summarizes and tabulates all available specific data on 2.25-mm DES. Based on our descriptive analysis, 2.25-mm DESs have a favorable safety and efficacy profile for the treatment of very small coronary lesions. - Highlights: • Safety and efficacy of 2.25-mm DES have been poorly defined. • We performed a systematic review on all published 2.25 mm data to estimate composite DES-specific performance and highlight current knowledge gaps. • We pooled data from 9 clinical studies and 1

Composite outcomes in 2.25-mm drug eluting stents: a systematic review

Energy Technology Data Exchange (ETDEWEB)

Lee, Justin Z. [Department of Medicine, University of Arizona, 1501 N Campbell Avenue, Tucson, AZ, 85724 (United States); Singh, Nirmal [Department of Cardiovascular Diseases, University of Arizona, 1501 N Campbell Ave, Tucson, AZ, 85724 (United States); Ortega, Gilbert [College of Medicine, University of Arizona, 1501 N Campbell Ave, Tucson, AZ, 85724 (United States); Low, See Wei; Kanakadandi, Uday [Department of Cardiovascular Diseases, University of Arizona, 1501 N Campbell Ave, Tucson, AZ, 85724 (United States); Fortuin, F. David [Department of Cardiovascular Diseases, Mayo Clinic Arizona, 5777 East Mayo Boulevard, Phoenix, AZ, 85054 (United States); Lassar, Tom [Department of Cardiovascular Diseases, University of Arizona, 1501 N Campbell Ave, Tucson, AZ, 85724 (United States); Lee, Kwan S., E-mail: klee@shc.arizona.edu [Department of Cardiovascular Diseases, University of Arizona, 1501 N Campbell Ave, Tucson, AZ, 85724 (United States)

2015-06-15

Background: Coronary atherosclerosis often involves small-caliber coronaries, yet the safety and efficacy of 2.25-mm DES have been poorly defined, with a general lack of separation of 2.25 with 2.5-mm performance. No randomized head-to-head 2.25 mm DES studies have been reported. There are several single-arm prospective studies, and we aim to systematically review all published specific 2.25-mm data to estimate composite DES-specific performance and highlight current knowledge gaps. Methods: We performed a systematic literature search of PubMed, EMBASE, Web of Science and Cochrane database for clinical trials of 2.25-mm DES. Angiographic and composite clinical outcomes were compared with descriptive statistics. Results: 2.25 mm-Paclitaxel (PES), sirolimus (SES), everolimus (EES) and platinum chromium EES DES-specific outcomes have been reported. Death at 12 months for SES, PES, EES and platinum chromium EES was 1.3%, 3.0%, 1.5%, and 4.4%. Rates of target vessel revascularization at 12 months for SES, PES, EES and platinum chromium EES were 5.7%, 13.3%, 8.8%, and 3.3%. Angiographic outcomes at 9 months to one year were as follows: mean late lumen loss (LLL) for SES, PES, and EES was 0.15 ± 0.11-mm, 0.28 ± 0.11-mm, and 0.16 ± 0.41-mm and mean diameter restenosis for SES, PES, and EES were 29.5 ± 6.2%, 34.7 ± 4.2%, and 20.9 ± 22.5%. Reported stent thrombosis rates for 2.25-mm DES were low ranging from 0% to 2.2% in up to 24-months of follow-up. Conclusions: This systematic review summarizes and tabulates all available specific data on 2.25-mm DES. Based on our descriptive analysis, 2.25-mm DESs have a favorable safety and efficacy profile for the treatment of very small coronary lesions. - Highlights: • Safety and efficacy of 2.25-mm DES have been poorly defined. • We performed a systematic review on all published 2.25 mm data to estimate composite DES-specific performance and highlight current knowledge gaps. • We pooled data from 9 clinical studies and 1

Mass-induced sea level variations in the Red Sea from steric-corrected altimetry, GRACE, in-situ bottom pressure records, and hydrographic observations

Science.gov (United States)

Feng, Wei; Lemoine, Jean-Michel; Zhong, Min; Xu, Houze

2014-05-01

An annual amplitude of ~18 cm mass-induced sea level variations (SLV) in the Red Sea is detected from steric-corrected altimetry and the Gravity Recovery and Climate Experiment (GRACE) satellites from 2003 to 2011, which dominates the mean sea level in the region. Seawater mass variations here generally reach maximum in late January/early February. The steric component of SLV calculated from oceanographic temperature and salinity data is relatively small and peaks about seven months later than mass variations. The phase difference between the steric SLV and the mass-induced SLV indicates that when the Red Sea gains the mass from inflow water in winter, the steric SLV fall, and vice versa in summer. In-situ bottom pressure records in the eastern coast of the Red Sea validate the high mass variability observed by steric-corrected altimetry and GRACE. Furthermore, we compare the horizontal water mass flux in the Red Sea from steric-corrected altimetry and GRACE with that estimated from hydrographic observations.

Test of freonless operation of resistive plate chambers with glass electrodes--1 mm gas gap vs 2 mm gas gap

CERN Document Server

Sakaue, H; Takahashi, T; Teramoto, Y

2002-01-01

Non-freon gas mixtures (Ar/iso-C sub 4 H sub 1 sub 0) were tested as the chamber gas for 1 and 2 mm gas gap Resistive Plate Chambers (RPCs) with float glass as the resistive electrodes, operated in the streamer mode. With the narrower (1 mm) gas gap, streamer charge is reduced (approx 1/3), which reduces the dead time (and dead area), associated with each streamer, improving the detection efficiency. The best performance was obtained for two cases: Ar/iso-C sub 4 H sub 1 sub 0 =50/50 and 60/40. For the 50/50 mixture, a detection efficiency of better than 98% was obtained for the 1 mm gap RPC, while the efficiency was 95% for the 2 mm gap RPC, each operated as a double-gap RPC. The measured time resolution (rms) was 1.45+-0.05 (2.52+-0.09) ns for the 1 (2) mm gap RPC for the 50/50 mixture.

A Novel Mechanism of Sugar Selection Utilized by a Human X-family DNA Polymerase†

OpenAIRE

Brown, Jessica A.; Fiala, Kevin A.; Fowler, Jason D.; Sherrer, Shanen M.; Newmister, Sean A.; Dyum, Wade W.; Suo, Zucai

2009-01-01

During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2′-hydroxyl group and the bulky side chain of an active site residue. Here, we demonstrated that human DNA polymerase λ used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2′-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such a steric clash was further demonst...

Abaxial growth and steric constraints guide leaf folding and shape in Acer pseudoplatanus.

Science.gov (United States)

Couturier, Etienne; Brunel, Nicole; Douady, Stéphane; Nakayama, Naomi

2012-08-01

How leaf shape is regulated is a long-standing question in botany. For diverse groups of dicotyledon species, lamina folding along the veins and geometry of the space available for the primordia can explain the palmate leaf morphology. Dubbed the kirigami theory, this hypothesis of fold-dependent leaf shape regulation has remained largely theoretical. Using Acer pseudoplatanus, we investigated the mechanisms behind the two key processes of kirigami leaf development. Cytological examination and quantitative analyses were used to examine the course of the vein-dependent lamina folding. Surgical ablation and tissue culturing were employed to test the effects of physical constraints on primordia growth. The final morphology of leaves growing without steric constraints were predicted mathematically. The cytological examination showed that the lamina's abaxial side along the veins grows substantially more than the adaxial side. The abaxial hypergrowth along the veins and the lamina extension correlated with the lamina folding. When a primordium was released from the physical constraints imposed by the other primordia, it rapidly grew into the newly available space, while maintaining the curvature inward. The morphology of such a leaf was predicted to lack symmetry in the lobe shapes. The enhanced growth on the abaxial side of the lamina along the veins is likely to drive lamina folding. The surgical ablation provided clear support for the space-filling nature of leaf growth; thus, steric constraints play a role in determination of the shapes of folded leaves and probably also of the final leaf morphology.

Reversible Redox-Induced Modulation of Sterics in an α-Diimine Ligand Coordinated to Gallium

Energy Technology Data Exchange (ETDEWEB)

Zarkesh, Ryan A. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Foster, Michael E. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Ichimura, Andrew S. [San Francisco State Univ., CA (United States); Anstey, Mitchell R. [Davidson College, Davidson, NC (United States)

2017-07-01

The ability to tune the steric envelope through redox events post-synthetically or in tandem with other chemical processes is a powerful tool that could assist in enabling new catalytic methodologies and understanding potential pitfalls in ligand design. The α-diimine ligand, dmp-BIAN, exhibits the peculiar and previously unreported feature of varying steric profiles depending on oxidation state when paired with a main group element. A study of the factors that give rise to this behaviour as well as its impact on the incorporation of other ligands is performed.

Metal-Free Approaches to Sterically-Hindered Bonds

Science.gov (United States)

Dunham, Veronica Vin-yi

Developing methods to perform cross coupling reactions by means of catalysis is highly desirable in chemistry. Many industries in today's society, such as the petroleum, agriculture, pharmaceutical, electronics, and polymer industry, use catalysis to some extent whether it is to make molecules that offer crop protection or toward the synthesis of the active ingredient of a medication. It is noteworthy that over 90% of chemicals are made through catalytic processes and that the catalyst market reached $17 billion in 2014, which demonstrates the demand for such methods. While transition metal catalysts have advantages such as low catalyst loading, broad reactivity, and that they have been well studied, some disadvantages are that they can be relatively expensive and sometimes air sensitive which can make them challenging to use. Organocatalysis, specifically noncovalent catalysis operating through hydrogen bond donating interactions, offers an environmentally-friendly alternative to transition metal catalysis. Our lab utilizes organocatalysis as a strategy to synthesize challenging, sterically-hindered bonds. Nitrimines have been identified as powerful coupling partners for the sustainable construction of new sterically congested carbon-carbon and carbon-heteroatom bonds. Using urea catalysis, a metal-free method to synthesize previously inaccessible enamines has been developed. Conventional routes to synthesize enamines as important building blocks toward target molecules generally require Lewis/Bronsted acids or expensive transition metals; however, these methods are often unsuccessful when stericallyhindered substrates are used. To address this synthetic challenge, it was hypothesized that hydrogen bonding interactions between a urea organocatalyst and nitrimine would generate a reactive species suited for the effective carbon-nitrogen coupling with amines to give the desired enamine products. This reaction provides high yields (up to 99%) of enamines using a

Steric Stabilization of “Charge-Free” Cellulose Nanowhiskers by Grafting of Poly(ethylene glycol

Directory of Open Access Journals (Sweden)

Jun Araki

2014-12-01

Full Text Available A sterically stabilized aqueous suspension of “charge-free” cellulose nanowhiskers was prepared by hydrochloric acid hydrolysis of cotton powders and subsequent surface grafting of monomethoxy poly(ethylene glycol (mPEG. The preparation scheme included carboxylation of the terminal hydroxyl groups in mPEG via oxidation with silica gel particles carrying 2,2,6,6-tetramethyl-1-pyperidinyloxyl (TEMPO moieties and subsequent esterification between terminal carboxyls in mPEG and surface hydroxyl groups of cellulose nanowhiskers, mediated by 1,1'-carbonyldiimidazole (CDI in dimethyl sulfoxide or dimethylacetamide. Some of the prepared PEG-grafted samples showed remarkable flow birefringence and enhanced stability after 24 h, even in 0.1 M NaCl, suggesting successful steric stabilization by efficient mPEG grafting. Actual PEG grafting via ester linkages was confirmed by attenuated total reflectance-Fourier transform infrared spectrometry. In a typical example, the amount of grafted mPEG was estimated as ca. 0.3 g/g cellulose by two measurements, i.e., weight increase after grafting and weight loss after alkali cleavage of ester linkages. Transmission electron microscopy indicated unchanged nanowhisker morphology after mPEG grafting.

Comparative evaluation of 2.3 mm locking plate system vs conventional 2.0 mm non locking plate system for mandibular condyle fracture fixation: a seven year retrospective study.

Science.gov (United States)

Zhang, J; Wang, X; Wu, R-H; Zhuang, Q-W; Gu, Q P; Meng, J

2015-01-01

This retrospective study evaluated the efficacy of a 2.3 mm locking plate/screw system compared with a 2.0-mm non-locking plate/screw system in fixation of isolated non comminuted mandibular condyle fractures. Surgical records of 101 patients who received either a 2.3 mm locking plate (group A, n = 51) or 2.0 mm non locking plate (group B, n = 50) were analyzed. All patients were followed up to a minimum of 6 months postoperatively and evaluated for hardware related complications, occlusal stability, need for and duration of MMF and mandibular functional results. Four complications occurred in the locking group and eighteen in the non locking group with complication rates equalling 8% and 36% respectively. When comparing the overall results according to plates used, the χ2 test showed a statistically significant difference between the locking and non locking plates (p Mandibular condyle fractures treated with a 2.3 mm locking plate exhibited stable osteosynthesis, were associated with minimal complications and resulted in acceptable mandibular range of motion compared with a 2.0 mm non locking plate.

A positron tomograph with 600 BGO crystals and 2.6 mm resolution

International Nuclear Information System (INIS)

Derenzo, S.E.; Huesman, R.H.; Cahoon, J.L.; Geyer, A.B.; Moses, W.W.; Uber, D.C.; Vuletich, T.; Budinger, T.F.

1988-01-01

The authors describe the imaging performance of the Donner 600-Crystal Positron Tomograph, a single 60 cm diam ring of 3 mm wide bismuth germanate (BGO) crystals coupled individually to 14 mm phototubes. With a pulse height threshold of 200 keV and a slice thickness of 5 mm, the sensitivity is 7024 events/sec per μCi/ml in a 20 cm cylinder of water. The measured rates for 18 μCi/ml are 95,000 trues/sec plus 20,000 random/sec. A 0.3 mm diam /sup 22/Na line source near the center of the tomograph has a circular point spread function (PSF) with a full-width at half-maximum (fwhm) of 2.6 mm. At 5 cm from the center the PSF is elliptical with a fwhm of 2.7 mm tangential x 3.2 mm radial. At 10 cm the PSF has a fwhm of 2.8 mm tangential x 4.8 mm radial. Attenuation data are accumulated with a 20 mCi /sup 68/Ge orbiting transmission source and 100 million coincident events are collected in 200 sec

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

DEFF Research Database (Denmark)

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob

2018-01-01

embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed......Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable...... at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdWTSexpression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We...

Revisiting the contemporary sea-level budget on global and regional scales.

Science.gov (United States)

Rietbroek, Roelof; Brunnabend, Sandra-Esther; Kusche, Jürgen; Schröter, Jens; Dahle, Christoph

2016-02-09

Dividing the sea-level budget into contributions from ice sheets and glaciers, the water cycle, steric expansion, and crustal movement is challenging, especially on regional scales. Here, Gravity Recovery And Climate Experiment (GRACE) gravity observations and sea-level anomalies from altimetry are used in a joint inversion, ensuring a consistent decomposition of the global and regional sea-level rise budget. Over the years 2002-2014, we find a global mean steric trend of 1.38 ± 0.16 mm/y, compared with a total trend of 2.74 ± 0.58 mm/y. This is significantly larger than steric trends derived from in situ temperature/salinity profiles and models which range from 0.66 ± 0.2 to 0.94 ± 0.1 mm/y. Mass contributions from ice sheets and glaciers (1.37 ± 0.09 mm/y, accelerating with 0.03 ± 0.02 mm/y(2)) are offset by a negative hydrological component (-0.29 ± 0.26 mm/y). The combined mass rate (1.08 ± 0.3 mm/y) is smaller than previous GRACE estimates (up to 2 mm/y), but it is consistent with the sum of individual contributions (ice sheets, glaciers, and hydrology) found in literature. The altimetric sea-level budget is closed by coestimating a remaining component of 0.22 ± 0.26 mm/y. Well above average sea-level rise is found regionally near the Philippines (14.7 ± 4.39 mm/y) and Indonesia (8.3 ± 4.7 mm/y) which is dominated by steric components (11.2 ± 3.58 mm/y and 6.4 ± 3.18 mm/y, respectively). In contrast, in the central and Eastern part of the Pacific, negative steric trends (down to -2.8 ± 1.53 mm/y) are detected. Significant regional components are found, up to 5.3 ± 2.6 mm/y in the northwest Atlantic, which are likely due to ocean bottom pressure variations.

A Novel Mechanism of Sugar Selection Utilized by a Human X-family DNA Polymerase†

Science.gov (United States)

Brown, Jessica A.; Fiala, Kevin A.; Fowler, Jason D.; Sherrer, Shanen M.; Newmister, Sean A.; Dyum, Wade W.; Suo, Zucai

2009-01-01

During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2′-hydroxyl group and the bulky side chain of an active site residue. Here, we demonstrated that human DNA polymerase λ used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2′-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such a steric clash was further demonstrated to be dependent on the size and orientation of the substituent covalently attached at the ribonucleotide C2′ position. PMID:19900463

Tuning and Quantifying Steric and Electronic Effects of N-Heterocyclic Carbenes

KAUST Repository

Falivene, Laura; Poater, Albert; Cavallo, Luigi

2014-01-01

This chapter states that the main handles for tuning steric and electronic effects are the substituents on N atoms, the nature of the C4-C5 bridge (either saturated or unsaturated), and the substituents on the C4 and C5 atoms. The initial intuition

A novel steric effect-regulated isothermal exponential amplification technology for the one-step homogeneous sensing of proteins.

Science.gov (United States)

Wu, Wanghua; Pan, Wufan; Yu, Dongdong; Yuan, Zhen; Qin, Yazhou; Lu, Yuxiang; Zhang, Tao; Zhou, Jianguang

2018-02-12

A simple and homogeneous technology, the steric effect-regulated isothermal exponential amplification reaction (SER-EXPAR), was developed to sense proteins. By using a small molecule linked DNA nanostructure, termed enzyme-binding hairpin (EBH), the protein-small molecule binding events could be readily sensed by utilizing the steric effect generated between the protein and enzyme. It set free the enzyme to be active again, thus regulating the amplification rate of EXPAR.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

Science.gov (United States)

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Mass-induced sea level variations in the Red Sea from GRACE, steric-corrected altimetry, in situ bottom pressure records, and hydrographic observations

Science.gov (United States)

Feng, W.; Lemoine, J.-M.; Zhong, M.; Hsu, H. T.

2014-08-01

An annual amplitude of ∼18 cm mass-induced sea level variations (SLV) in the Red Sea is detected from the Gravity Recovery and Climate Experiment (GRACE) satellites and steric-corrected altimetry from 2003 to 2011. The annual mass variations in the region dominate the mean SLV, and generally reach maximum in late January/early February. The annual steric component of the mean SLV is relatively small (mass-induced SLV. In situ bottom pressure records at the eastern coast of the Red Sea validate the high mass variability observed by steric-corrected altimetry and GRACE. In addition, the horizontal water mass flux of the Red Sea estimated from GRACE and steric-corrected altimetry is validated by hydrographic observations.

Role of Steric Hindrance in the Crystal Packing of Z′ = 4 Superstructure of Trimethyltin Hydroxide

KAUST Repository

Dey, S.

2018-01-22

The roomerature crystal structure of trimethyltin hydroxide, (CH)SnOH, has been described by Anderson et al. [Cryst. Growth Des. 2011, 11, 820-826] as a 2a × 2b × 8c, 32-fold superstructure. We report a a × b × 8c, eight-fold superstructure with orthorhombic P2cn symmetry and Z′ = 4. Structured diffuse scattering observed at the positions of presumed superlattice reflections along a∗ and b∗ might have appeared as Bragg reflections in the experiment by Anderson et al. Alternatively, Anderson et al. and the present work might have studied different polymorphs of (CH)SnOH. Crystalline (CH)SnOH constitutes polymeric chains arranged parallel to c. In the eight-fold superstructure at 220 K, the polymeric chains possess a distorted zigzag arrangement of linked linear O-Sn-O units with bent angle at oxygen of ∼139.2°. This structure is essentially different from the 8-helical arrangement in the published 32-fold superstructure model. The origin of the distorted zigzag structure is explained by steric hindrance between hydrogen atoms of adjacent hydroxy groups and (CH)Sn groups. Frustration in the packing of the chains is determined by steric hindrance between methyl groups of neighboring chains, which prevents the formation of interchain C-H···O hydrogen bonds.

Remote Steric Effect as a Facile Strategy for Improving the Efficiency of Exciplex-Based OLEDs.

Science.gov (United States)

Hung, Wen-Yi; Wang, Ting-Chih; Chiang, Pin-Yi; Peng, Bo-Ji; Wong, Ken-Tsung

2017-03-01

This work reports a new strategy of introducing remote steric effect onto the electron donor for giving the better performance of the exciplex-based organic light-emitting device (OLED). The bulky triphenylsilyl group (SiPh 3 ) was introduced onto the fluorene bridge of 4,4'-(9H-fluorene-9,9-diyl)bis(N,N-di-p-tolylaniline) (DTAF) to create remote steric interactions for increasing the possibility of effective contacts between electron-donating chromophores and acceptor molecules, rendering the resulting exciplex to have a higher photoluminescence quantum yield (PLQY). The green exciplex device based on DSDTAF:3N-T2T (1:1) as an emitting layer exhibits a low turn-on voltage of 2.0 V, high maximum efficiencies (13.2%, 42.9 cd A -1 , 45.5 lm W -1 ), which are higher than the device employed DTAF (without SiPh 3 groups) (11.6%, 35.3 cd A -1 , 41.3 lm W -1 ) as donor under the same device structure. This strategy was further examined for blue exciplex, where the EQE was enhanced from 9.5% to 12.5% as the electron acceptor PO-T2T mixed with a tert-butyl group substituted carbazole-based donor (CPTBF) as the emitting exciplex in device. This strategy is simple and useful for developing high performance exciplex OLEDs.

Electromagnetic and mechanical design of a 56 mm aperture mode dipole for the LHC

International Nuclear Information System (INIS)

Ahlbaeck, J.; Ikaeheimo, J.; Jaervi, J.

1994-01-01

The Large Hadron Collider (LHC) project is proposed as the future extension of the CERN accelerator complex. The LHC requires twin aperture superconducting dipoles of highest possible field to guide the proton beams in the existing LEP tunnel of 26.7 km circumference. This paper describes the electromagnetic and mechanical design of a 56 mm aperture model dipole for the LHC

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

Science.gov (United States)

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Steric hindrances create a discrete linear Dy4 complex exhibiting SMM behaviour.

Science.gov (United States)

Lin, Shuang-Yan; Zhao, Lang; Ke, Hongshan; Guo, Yun-Nan; Tang, Jinkui; Guo, Yang; Dou, Jianmin

2012-03-21

Two linear tetranuclear lanthanide complexes of general formula [Ln(4)(L)(2)(C(6)H(5)COO)(12)(MeOH)(4)], where HL = 2,6-bis((furan-2-ylmethylimino)methyl)-4-methylphenol, () and Ln(III) = Dy(III) (1) and Gd(III) (2), have been synthesized and characterized. The crystal structural analysis demonstrates that two Schiff-base ligands inhibit the growth of benzoate bridged 1D chains, leading to the isolation of discrete tetranuclear complexes due to their steric hindrances. Every Ln(III) ion is coordinated by eight donor atoms in a distorted bicapped trigonal-prismatic arrangement. Alternating current (ac) susceptibility measurements of complex 1 reveal a frequency- and temperature-dependent out-of-phase signal under zero dc field, typical of single-molecule magnet (SMM) behaviour with an anisotropic barrier Δ(eff) = 17.2 K.

Different Steric-Twist-Induced Ternary Memory Characteristics in Nonconjugated Copolymers with Pendant Naphthalene and 1,8-Naphthalimide Moieties.

Science.gov (United States)

Wang, Ming; Li, Zhuang; Li, Hua; He, Jinghui; Li, Najun; Xu, Qingfeng; Lu, Jianmei

2017-10-18

Herein, novel random copolymers PMNN and PMNB were designed and synthesized, and the memory devices Al/PMNN and PMNB/ITO both exhibited ternary memory performance. The switching voltages of the OFF-ON1 and ON1-ON2 transitions for both memory devices are around -2.0 and -3.5 V, respectively, and the ON1/OFF, ON2/ON1 current ratios are both up to 10 3 . The observed tristable electrical conductivity switching could be attributed to field-induced conformational ordering of the naphthalene rings in the side chains, and subsequent charge trapping by 1,8-naphthalimide moieties. More interestingly, by adjusting the connection sites of 1,8-naphthalimide moieties to tune the steric-twist effect, different memory properties were achieved (PMNN showed nonvolatile write once, read many (WORM) memory behavior, whereas PMNB showed volatile static RAM (SRAM) memory behavior). This result will offer a guideline for the design of different high-performance multilevel memory devices by tuning the steric effects of the chemical moieties. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Calculation of Standard Enthalpies of Formation of Alkanes: Illustrating Molecular Mechanics and Spreadsheet Programs

Science.gov (United States)

Hawk, Eric Leigh

1999-02-01

How group increment methods may be used to predict standard enthalpies of formation of alkanes is outlined as an undergraduate computational chemistry experiment. The experiment requires input and output data sets. Although users may create their own data sets, both sets are provided. The input data set contains experimentally determined gas-phase standard enthalpies of formation and calculated steric energies for 10 alkanes. The steric energy for an alkane is calculated via a Molecular Mechanics approach employing Allinger's MM3 force field. Linear regression analysis on data contained in the input data set generates the coefficients that are used with the output data set to calculate standard enthalpies of formation for 15 alkanes. The average absolute error for the calculated standard enthalpies of formation is 1.22 kcal/mol. The experiment is highly suited to those interested in incorporating more computational chemistry in their curricula. In this regard, it is ideally suited for a physical chemistry laboratory, but it may be used in an organic chemistry course as well.

Steric and electronic effects of 1,3-disubstituted cyclopentadienyl ligands on metallocene derivatives of Cerium, Titanium, Manganese, and Iron

Energy Technology Data Exchange (ETDEWEB)

Sofield, Chadwick Dean [Univ. of California, Berkeley, CA (United States)

2000-05-01

Sterically demanding 1,3-disubstituted cyclopentadienyl ligands were used to modify the physical properties of the corresponding metallocenes. Sterically demanding ligands provided kinetic stabilization for trivalent cerium compounds. Tris(di-t-butylcyclopentadienyl)cerium was prepared and anion competition between halides and cyclopentadienyl groups which had complicated synthesis of the tris(cyclopentadienyl)compound was qualitatively examined. Bis(di-t-butylcyclopentadienyl)cerium methyl was prepared and its rate of decomposition, by ligand redistribution, to tris(di-t-butylcyclopentadienyl)cerium was shown to be slower than the corresponding rate for less sterically demanding ligands. Asymmetrically substituted ligands provided a symmetry label for examination of chemical exchange processes. Tris[trimethylsilyl(t-butyl)cyclopentadienyl]cerium was prepared and the rate of interconversion between the C1 and C3 isomers was examined. The enthalpy difference between the two distereomers is 7.0 kJ/mol. The sterically demanding cyclopentadienyl ligands ansa-di-t-butylcyclopentadiene (Me₂Si[(Me₃C)₂C₅H₃]₂), ansa-bis(trimethylsilyl)cyclopentadiene (Me₂Si[(Me₃Si)₂C₅H₃]₂) and tetra-t-butylfulvalene and metallocene derivatives of the ligands were prepared and their structures were examined by single crystal X-ray crystallography. The effect that substituents on the cyclopentadienyl ring have on the pi-electron system of the ligand was examined through interaction between ligand and metal orbitals. A series of 1,3-disubstituted manganocenes was prepared and their electronic states were determined by solid-state magnetic susceptibility, electron paramagnetic resonance, X-ray crystallography, and variable temperature UV-vis spectroscopy. Spin-equilibria in [(Me₃C)₂C₅H₃]₂Mn and [(Me₃

A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

Science.gov (United States)

Lv, Jing; Zhang, Jingxue; Wang, Dunyou

2016-02-17

We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

1st International Conference of IFToMM Italy

CERN Document Server

Gasparetto, Alessandro

2017-01-01

This volume contains the Proceedings of the First International Conference of IFToMM Italy (IFIT2016), held at the University of Padova, Vicenza, Italy, on December 1-2, 2016. The book contains contributions on the latest advances on Mechanism and Machine Science. The fifty-nine papers deal with such topics as biomechanical engineering, history of mechanism and machine science, linkages and mechanical controls, multi-body dynamics, reliability, robotics and mechatronics, transportation machinery, tribology, and vibrations.

A positron tomograph with 600 BGO [bismuth germanate] crystals and 2.6 mm resolution

International Nuclear Information System (INIS)

Derenzo, S.E.; Huesman, R.H.; Cahoon, J.L.; Geyer, A.B.; Moses, W.W.; Uber, D.C.; Vuletich, T.; Budinger, T.F.

1987-10-01

We describe the imaging performance of the Donner 600-Crystal Positron Tomograph, a single 600 cm diam ring of 3 mm wide bismuth germanate (BGO) crystals coupled individually to 14 mm phototubes. With a pulse height threshold of 200 keV and a slice thickness of 5 mm, the sensitivity is 7024 eventssec per μCiml in a 20 cm cyliner of water. The measured rates for 18 μCiml are 95,000 truessec plus 20,000 randomsec. A 0.3 mm diam 22 Na line source near the center of the tomograph has a circular point spread function (PSF) with a full-width at half-maximum (fwhm) of 2.6 mm. At 5 cm from the center the PSF is elliptical with a fwhm of 2.7 mm tangential /times/ 3.2 mm radial. At 10 cm the PSF has a fwhm of 2.8 mm tangential /times/ 4.8 mm radial. Attenuation data are accumulated with a 20 mCi 68 Ge orbiting transmission source and 100 million coincident events are collected in 200 sec. 20 refs., 9 figs., 5 tabs

Dye stability and performances of dye-sensitized solar cells with different nitrogen additives at elevated temperatures - Can sterically hindered pyridines prevent dye degradation?

Energy Technology Data Exchange (ETDEWEB)

Tuyet Nguyen, Phuong; Lund, Torben [Department of Science, Systems and Models, Roskilde University, 4000 Roskilde (Denmark); Rand Andersen, Anders [University of Southern Denmark, Institute of Sensors, Signals and Electrotechnics (SENSE), Niels Bohrs Alle 1, 5230 Odense M (Denmark); Danish Technological Institute, Plastics Technology, Gregersensvej 2630 Taastrup (Denmark); Morten Skou, Eivind [University of Southern Denmark, Department of Chemical Engineering, Biotechnology and Enviromental Technology, Niels Bohrs Alle 1, 5230 Odense M (Denmark)

2010-10-15

The homogeneous kinetics of the nucleophilic substitution reactions between the ruthenium dye N719 and eight pyridines and 1-methylbenzimidazole have been investigated in 3-methoxypropionitrile at 100 C. The half lives of N719 with the additives 4-tert-butylpyridine (0.5 M) and 1-methylbenzimidazole (0.5 M) were 57 and 160 h, respectively. Sterically hindered pyridines like 2,6-lutidine did not react with N719. The efficiencies of dye-sensitized solar cells (DSC, area=8.0 cm{sup 2}) prepared with 1-methylbenzimidazole (MBI), 4-tert-butylpyridine (4-TBP), 2,6-lutidine and without any additive were 7.1%, 6.2%, 6.0% and 4.8%, respectively. The cells were stored in dark at 85 C and their I-V curves and impedance spectra were measured at regular time intervals. The N719 dye degradation in the cells were monitored by a new dye extraction protocol combined with analysis of the dye extract by HPLC coupled to mass spectrometry. After 300 h storage in dark at 85 C 40% of the initial amount of N719 dye was degraded in DSC cells prepared with MBI and the efficiency was decreased to 40% of its initial value. DSC cells prepared with 2,6-lutidine or no additives showed smaller thermal dye and efficiency stability at elevated temperatures than DSC cells prepared with the none sterically hindered additives MBI and 4-TBP. In the cells prepared with 2,6-lutidine or no additive higher contents of the iodo products [RuL{sub 2}(NCS)(iodide)]{sup +} and [RuL{sub 2}(3-MPN)(iodide)]{sup +} were found than in cells prepared with 4-TBP and MBI. It is suggested that sterically hindered pyridines have smaller complexation constants with I{sub 3}{sup -} than unsterically hindered additives. This may explain the observed faster nucleophilic substitution rates of uncomplexed I{sub 3}{sup -} with N719 in DSC cells prepared with sterically hindered pyridines. The EIS analysis showed that the lifetime of the injected electrons in the TiO{sub 2}{tau}{sub eff} is reduced by a thermally induced change

Formation, thermal stability and mechanical properties of bulk glassy alloys with a diameter of 20 mm in Zr-(Ti,Nb)-Al-Ni-Cu system

International Nuclear Information System (INIS)

Inoue, A.; Zhang, Q.S.; Zhang, W.; Yubuta, K.; Son, K.S.; Wang, X.M.

2009-01-01

Bulk glassy alloy rods with a diameter of 20 mm were produced for Zr 61 Ti 2 Nb 2 Al 7.5 Ni 10 Cu 17.5 and Zr 60 Ti 2 Nb 2 Al 7.5 Ni 10 Cu 18.5 by a tilt casting method. The replacement of Zr by a small amount of Ti and Nb caused a distinct increase in the maximum diameter from 16 mm for Zr 65 Al 7.5 Ni 10 Cu 17.5 to 20 mm, accompanying the decrease in liquidus temperature and the increase in reduced glass transition temperature. The primary precipitation phase from supercooled liquid also shows a distinct change, i.e., from coexistent Zr 2 Cu, Zr 2 Ni and Zr 6 NiAl 2 phases for the 65%Zr alloy to an icosahedral phase for the 61%Zr and 60%Zr alloys. These results allow us to presume that the enhancement of the glass-forming ability is due to an increase in the stability of supercooled liquid against crystallization caused by the development of icosahedral short-range ordered atomic configurations. The 60%Zr specimens taken from the central and near-surface regions in the transverse cross section at the site which is 15 mm away from the bottom surface of the cast glassy rod with a diameter of 20 mm exhibit good mechanical properties under a compressive deformation mode, i.e., Young's modulus of 81 GPa, large elastic strain of 0.02, high yield strength of 1610 MPa and distinct plastic strain of 0.012. Besides, a number of shear bands are observed along the maximum shear stress plane on the peripheral surface near the final fracture site. The finding of producing the large scale Zr-based bulk glassy alloys exhibiting reliable mechanical properties is encouraging for future advancement of bulk glassy alloys as a new type of functional material. (author)

Design, Modelling and Teleoperation of a 2 mm Diameter Compliant Instrument for the da Vinci Platform.

Science.gov (United States)

Francis, P; Eastwood, K W; Bodani, V; Looi, T; Drake, J M

2018-05-07

This work explores the feasibility of creating and accurately controlling an instrument for robotic surgery with a 2 mm diameter and a three degree-of-freedom (DoF) wrist which is compatible with the da Vinci platform. The instrument's wrist is composed of a two DoF bending notched-nitinol tube pattern, for which a kinematic model has been developed. A base mechanism for controlling the wrist is designed for integration with the da Vinci Research Kit. A basic teleoperation task is successfully performed using two of the miniature instruments. The performance and accuracy of the instrument suggest that creating and accurately controlling a 2 mm diameter instrument is feasible and the design and modelling proposed in this work provide a basis for future miniature instrument development.

The catalytic mechanism of mouse renin studied with QM/MM calculations.

Science.gov (United States)

Brás, Natércia F; Ramos, Maria J; Fernandes, Pedro A

2012-09-28

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.

Symmetric tape round REBCO wire with J e (4.2 K, 15 T) beyond 450 A mm-2 at 15 mm bend radius: a viable candidate for future compact accelerator magnet applications

Science.gov (United States)

Kar, Soumen; Luo, Wenbo; Ben Yahia, Anis; Li, Xiaofen; Majkic, Goran; Selvamanickam, Venkat

2018-04-01

Round REBCO (RE = rare earth) wires of 1.6-1.85 mm diameter have been fabricated using ultrathin REBCO tapes where the superconductor film is positioned near the geometric center. Such symmetric tape round (STAR) wires exhibit excellent tolerance to bend strain with a critical current retention of more than 97% when bent to a radius of 15 mm. A 1.6 mm diameter REBCO STAR wire made with six 2.5 mm wide symmetric tapes reached an engineering current density (J e) of 454 A mm-2 at 4.2 K in a background field of 15 T at a bend radius of 15 mm. Such superior performance at a small bend radius can enable fabrication of future accelerator magnets, operating at magnetic fields above 20 T.

A molecular mechanics (MM3(96)) force field for metal-amide complexes

International Nuclear Information System (INIS)

Hay, B.P.; Clement, O.; Sandrone, G.; Dixon, D.A.

1998-01-01

A molecular mechanics (MM3(96)) force field is reported for modeling metal complexes of amides in which the amide is coordinated through oxygen. This model uses a points-on-a-sphere approach which involves the parameterization of the Msingle bondO stretch, the Msingle bondO double-bond C bend, and the Msingle bondO double-bond Csingle bondX (X = C, H, N) torsion interactions. Relationships between force field parameters and metal ion properties (charge, ionic radius, and electronegativity) are presented that allow the application of this model to a wide range of metal ions. The model satisfactorily reproduces the structures of over fifty amide complexes with the alkaline earths, transition metals, lanthanides, and actinides

Phospholipids chiral at phosphorus. Steric course of the reactions catalyzed by phosphatidylserine synthase from Escherichia coli and yeast

International Nuclear Information System (INIS)

Raetz, C.R.H.; Carman, G.M.; Dowhan, W.; Jiang, R.T.; Waszkuc, W.; Loffredo, W.; Tsai, M.D.

1987-01-01

The steric courses of the reactions catalyzed by phosphatidylserine (PS) synthase from Escherichia coli and yeast were elucidated by the following procedure. R/sub P/ and S/sub P/ isomers of 1,2-dipalmitoyl-sn-glycero-3-[ 17 O, 18 O]phosphoethanolamine ([ 17 O, 18 O]DPPE) were synthesized and converted to (R/sub P/)- and (S/sub P/)-1,2-dipalmitoyl-sn-glycero-3-[ 16 O, 17 O, 18 O]DPPA), respectively, by incubating with phospholipase D. Condensation of [ 16 O, 17 O, 18 O]DPPA with cytidine 5'-monophosphomorpholidate in pyridine gave the desired substrate for PS synthase, [ 17 O, 18 O]cytidine 5'-diphospho-1,2-dipalmitoyl-sn-glycerol ([ 17 O, 18 O]CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of [ 17 O, 18 O]CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of [ 17 O, 18 O] CDP-DPG with a mixture of L-serine, PS synthase and PS decarboxylase gave [ 17 O, 18 O]DPPE. The configuration and isotopic enrichments of the starting [ 17 O, 18 O]DPPE and the product were analyzed by 31 P NMR following trimethylsilylation of the DPPE. The results indicate that the reaction of E. coli PS synthase proceeds with retention of configuration at phosphorus, which suggests a two-step mechanism involving a phosphatidyl-enzyme intermediate, while the yeast PS synthase catalyzes the reaction with inversion of configuration, which suggests a single-displacement mechanism. Such results lend strong support to the ping-pong mechanism proposed for the E. coli enzyme and the sequential Bi-Bi mechanism proposed for the yeast enzyme, both based on previous isotopic exchange experiments

Intrinsic evolution of novel (Nd, MM)2Fe14B-system magnetic flakes

Science.gov (United States)

Yu, Xiaoqiang; Zhu, Minggang; Liu, Weiqiang; Li, Yanfeng; Zhang, Jiuxing; Yue, Ming; Li, Wei

2018-01-01

The Nd-substituted (Nd x MM1- x )-Fe-B strip-casting flakes were prepared by induction melting in the vacuum furnace and then subsequently by strip-casting technology. The microstructure and magnetic properties of (Nd x MM1- x )-Fe-B alloys are related to the Nd substitution. 2:14:1 main phases and minor impure phases coexist in the MM-Fe-B flake. For example, La2O3 and CeFe2 impure phases are obviously detected in the x = 0 specimen. As an increase of the Ce concentration is inversely accompanied with the decrease of the Nd content ( x) in (Nd x MM1- x )2Fe14B main phases (0 ≤ x ≤ 1), XRD analysis shows that the overall diffraction peaks of the main phases shift to right domestically because of smaller radius Ce4+. The melting point, spin reorientation phase transition temperature, Curie temperature, magneto-crystalline anisotropy field (at 300 K), and the magnetization ( M 9T) for MM-Fe-B/(Nd0.4MM0.6)-Fe-B/(Nd0.7MM0.3)-Fe-B/Nd-Fe-B strip-casting alloys are 1376.15/1414.15/1439.15/1458.15 K, 74/113/124/135 K, 493.2/538.4/559.7/582.3 K, 48/55.2/64.4/70.1 kOe and 136.5/143.7/151.5/153.7 emu/g, respectively. Due to the varied composition of hard magnetic main phases, M 9T increases gradually with the increase of Nd content ( x). SEM observation and EDX results demonstrate that more Nd and Pr elements aggregate into the 2:14:1 ferromagnetic phase, while less La and Ce elements are prone to the RE-rich region compared with the nominal ratio. As a result, the growth of M 9T becomes extraordinary under maximum external field 9 T, indicating that the (Nd0.7MM0.3)-Fe-B flake may display relatively good magnetic properties and those with higher Nd content have evident effect on magnetization, compositions, and microstructures of hard magnetic main phases. Therefore, practical application of (Nd x MM1- x )-Fe-B-sintered magnets will be very prospective.

Comparative analysis of corneal morphological changes after transversal and torsional phacoemulsification through 2.2 mm corneal incision.

Science.gov (United States)

Assaf, Ahmed; Roshdy, Maged Maher

2013-01-01

This paper compares and evaluates the corneal morphological changes occurring after cataract surgery through a 2.2 mm corneal incision. We use two platforms for comparison and evaluation, transversal and torsional phacoemulsification. This study includes 139 consecutive cataractous eyes (nuclear color 2-4, according to the Lens Opacities Classification System III [LOCSIII]) of 82 patients undergoing cataract surgery through a 2.2 mm corneal incision. Two different phacoemulsification platforms were used and assigned randomly: we used the WhiteStar Signature(®) system with the Ellips™ FX transversal continuous ultrasound (US) mode for group I (mean age: 65.33 ± 6.97 years), and we used the Infiniti(®) system with the OZil(®) Intelligent Phaco (IP) torsional US mode for group II (mean age: 64.02 ± 7.55 years). The corneal endothelium and pachymetry were evaluated preoperatively and at 1 month postoperatively. Incision size changes were also evaluated. All surgeries were uneventful. Before intraocular lens implantation, the mean incision size was 2.24 ± 0.06 mm in both groups (P = 0.75). In terms of corneal endothelial cell density, neither preoperative (I vs II: 2304.1 ± 122.5 cell/mm(2) vs 2315.6 ± 83.1 cell/mm(2), P = 0.80) nor postoperative (I vs II: 2264.1 ± 124.3 cell/mm(2) vs 2270.3 ± 89.9 cell/mm(2), P = 0.98) differences between the groups were statistically significant. The mean endothelial cell density loss was 1.7% ± 1.6% and 2.0% ± 1.4% in groups I and II, respectively. Furthermore, no significant differences between groups I and II were found preoperatively (P = 0.40) and postoperatively (P = 0.68) in central pachymetry. With surgery, the mean increase in central pachymetry was 28.1 ± 23.6 μm and 24.0 ± 24.0 μm in groups I and II, respectively (P = 0.1). Ellips™ FX transversal and OZil(®) IP torsional phacoemulsification modes are safe for performing cataract surgery, inducing minimal corneal thickness and endothelial changes.

Stereochemistry and mechanism of the reduction of some bicyclo (2-2-1-) heptane-2-ones by metals dissolved in liquid ammonia

International Nuclear Information System (INIS)

Coulombeau, A.

1969-01-01

A systematic experimental study of the reduction of four bicyclo(2-2-1)hepta n-2-ones by dissolved alkaline and alkaline-earth metals in liquid ammonia is reported. Chapter one: models of metal-ammonia solutions and mechanisms of the reduction of ketones by these solutions are rapidly recalled. Chapter two: results obtained in the thermodynamic equilibration of three pairs of epimeric alcohols which formally derive from three of the starting ketones are presented. Chapter three: deals with the results obtained in the reduction of the ketones in the absence or the presence of a proton source. A new interpretation of these results is given and is based upon two different effects: - the torsional interaction created by the bridgehead substituent on the C-O bond which favours the formation of the endo alcohol; - the difference of steric hindrance between the two sides (exo and endo) defined by the plane of the carbonyl group of the starting molecule, which favours the attack of the metal cation from one side or the other, and therefore the formation of the exo or the endo epimer. This mechanism is generalised in a model which is tested by means of some examples published in the literature. It then appears able to construe correctly the obtained results. (author) [fr

QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

Energy Technology Data Exchange (ETDEWEB)

Hagiwara, Yohsuke; Tateno, Masaru [Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571 (Japan); Ohta, Takehiro [Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8577 (Japan)], E-mail: tateno@ccs.tsukuba.ac.jp

2009-02-11

An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.

Steric Interference of Adhesion Supports In-Vitro Chondrogenesis of Mesenchymal Stem Cells on Hydrogels for Cartilage Repair

OpenAIRE

Goldshmid, Revital; Cohen, Shlomit; Shachaf, Yonatan; Kupershmit, Ilana; Sarig-Nadir, Offra; Seliktar, Dror; Wechsler, Roni

2015-01-01

Recent studies suggest the presence of cell adhesion motifs found in structural proteins can inhibit chondrogenesis. In this context, the current study aims to determine if a polyethylene glycol (PEG)-modified fibrinogen matrix could support better chondrogenesis of human bone marrow mesenchymal stem cells (BM-MSC) based on steric interference of adhesion, when compared to a natural fibrin matrix. Hydrogels used as substrates for two-dimensional (2D) BM-MSC cultures under chondrogenic conditi...

MM1+2C sporadic Creutzfeldt-Jakob disease presenting as rapidly progressive nonfluent aphasia.

Science.gov (United States)

Allegri, Ricardo F; Bartoloni, Leonardo; Iturry, Mónica; Romero, Carlos; Begué, Christián; Sevlever, Gustavo; Taratuto, Ana Lía

2014-01-01

We report a 77-year-old man, presenting with progressive aphasia as an initial symptom, who developed severe dementia over the course of 20 months. Frontal cortex PrPSc western blot was type 2 and codon 129 was MM; brain neuropathology showed cortical vacuoles with perivacuolar PrP immunostaining characteristic of MM2C. Cerebellum showed focal coarse, patchy staining in different sections of the molecular layer, diffuse fine punctuate and coarse PrP immunopositive deposits in the granule cell layer, and focal synaptic immunostaining in the molecular layer, suggestive of MM1+2C by histotyping. This clinical presentation has not yet been described in an MM1+2C subtype by histotyping.

Comparative analysis of corneal morphological changes after transversal and torsional phacoemulsification through 2.2 mm corneal incision

Directory of Open Access Journals (Sweden)

Assaf A

2013-01-01

Full Text Available Ahmed Assaf, Maged Maher RoshdyOphthalmology Department, Ain Shams University, Cairo, EgyptPurpose: This paper compares and evaluates the corneal morphological changes occurring after cataract surgery through a 2.2 mm corneal incision. We use two platforms for comparison and evaluation, transversal and torsional phacoemulsification.Patients and methods: This study includes 139 consecutive cataractous eyes (nuclear color 2–4, according to the Lens Opacities Classification System III [LOCSIII] of 82 patients undergoing cataract surgery through a 2.2 mm corneal incision. Two different phacoemulsification platforms were used and assigned randomly: we used the WhiteStar Signature® system with the Ellips™ FX transversal continuous ultrasound (US mode for group I (mean age: 65.33 ± 6.97 years, and we used the Infiniti® system with the OZil® Intelligent Phaco (IP torsional US mode for group II (mean age: 64.02 ± 7.55 years. The corneal endothelium and pachymetry were evaluated preoperatively and at 1 month postoperatively. Incision size changes were also evaluated.Results: All surgeries were uneventful. Before intraocular lens implantation, the mean incision size was 2.24 ± 0.06 mm in both groups (P = 0.75. In terms of corneal endothelial cell density, neither preoperative (I vs II: 2304.1 ± 122.5 cell/mm2 vs 2315.6 ± 83.1 cell/mm2, P = 0.80 nor postoperative (I vs II: 2264.1 ± 124.3 cell/mm2 vs 2270.3 ± 89.9 cell/mm2, P = 0.98 differences between the groups were statistically significant. The mean endothelial cell density loss was 1.7% ± 1.6% and 2.0% ± 1.4% in groups I and II, respectively. Furthermore, no significant differences between groups I and II were found preoperatively (P = 0.40 and postoperatively (P = 0.68 in central pachymetry. With surgery, the mean increase in central pachymetry was 28.1 ± 23.6 µm and 24.0 ± 24.0 µm in groups I and II, respectively (P = 0.1.Conclusion: Ellips™ FX transversal and OZil® IP torsional

Hydrophilic luminescent silicon nanoparticles in steric colloidal solutions: their size, agglomeration and toxicity

Czech Academy of Sciences Publication Activity Database

Herynková, Kateřina; Šimáková, Petra; Cibulka, Ondřej; Fučíková, Anna; Kalbáčová, M.H.

2017-01-01

Roč. 14, č. 12 (2017), s. 1-4, č. článku 1700195. ISSN 1862-6351 Grant - others:AV ČR(CZ) DAAD-16-18 Program:Bilaterální spolupráce Institutional support: RVO:68378271 Keywords : silicon nanocrystals * colloidal solutions * steric stabilization * cytotoxicity Subject RIV: BO - Biophysics OBOR OECD: Biophysics

Exploring electronic and steric effects on the insertion and polymerization reactivity of phosphinesulfonato pdii catalysts

KAUST Repository

Neuwald, Boris; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Mecking, Stefan

2013-01-01

incorporation at low MA concentrations in the copolymerization; and 3) steric shielding leads to a pronounced increase in polymer molecular weight in the copolymerization. The catalyst properties induced by a given P-aryl (alkyl) moiety were combined effectively

THE RADIO-2 mm SPECTRAL INDEX OF THE CRAB NEBULA MEASURED WITH GISMO

International Nuclear Information System (INIS)

Arendt, R. G.; George, J. V.; Staguhn, J. G.; Benford, D. J.; Fixsen, D. J.; Maher, S. F.; Moseley, S. H.; Sharp, E.; Wollack, E. J.; Devlin, M. J.; Dicker, S. R.; Korngut, P. M.; Irwin, K. D.; Jhabvala, C. A.; Miller, T. M.; Kovacs, A.; Mason, B. S.; Navarro, S.; Sievers, A.; Sievers, J. L.

2011-01-01

We present results of 2 mm observations of the Crab Nebula, obtained using the Goddard-IRAM Superconducting 2 Millimeter Observer (GISMO) bolometer camera on the IRAM 30 m telescope. Additional 3.3 mm observations with the MUSTANG bolometer array on the Green Bank Telescope are also presented. The integrated 2 mm flux density of the Crab Nebula provides no evidence for the emergence of a second synchrotron component that has been proposed. It is consistent with the radio power-law spectrum, extrapolated up to a break frequency of log (ν b [GHz]) = 2.84 ± 0.29 or ν b = 695 +651 -336 GHz. The Crab Nebula is well resolved by the ∼16.''7 beam (FWHM) of GISMO. Comparison to radio data at comparable spatial resolution enables us to confirm significant spatial variation of the spectral index between 21 cm and 2 mm. The main effect is a spectral flattening in the inner region of the Crab Nebula, correlated with the toroidal structure at the center of the nebula that is prominent in the near-IR through X-ray regime.

PWV, Temperature and Wind Statistics at Sites Suitable For mm and Sub-mm Wavelengths Astronomy

Science.gov (United States)

Otarola, Angel; Travouillon, Tony; De Breuck, Carlos; Radford, Simon; Matsushita, Satoki; Pérez-Beaupuits, Juan P.

2018-01-01

Atmospheric water vapor is the main limiting factor of atmospheric transparency in the mm and sub-mm wavelength spectral windows. Thus, dry sites are needed for the installation and successful operation of radio astronomy observatories exploiting those spectral windows. Other parameters that play an important role in the mechanical response of radio telescopes exposed to the environmental conditions are: temperature, and in particular temperature gradients that induce thermal deformation of mechanical structures, as well as wind magnitude that induce pointing jitter affecting this way the required accuracy in the ability to point to a cosmic source during the observations. Temperature and wind are variables of special consideration when planning the installation and operations of large aperture radio telescopes. This work summarizes the statistics of precipitable water vapor (PWV), temperature and wind monitored at sites by the costal mountain range, as well as on t he west slope of the Andes mountain range in the region of Antofagasta, Chile. This information could prove useful for the planning of the Atacama Large-Aperture Submm/mm Telescope (AtLast).

Steric restrictions of RISC in RNA interference identified with size-expanded RNA nucleobases.

Science.gov (United States)

Hernández, Armando R; Peterson, Larryn W; Kool, Eric T

2012-08-17

Understanding the interactions between small interfering RNAs (siRNAs) and the RNA-induced silencing complex (RISC), the key protein complex of RNA interference (RNAi), is of great importance to the development of siRNAs with improved biological and potentially therapeutic function. Although various chemically modified siRNAs have been reported, relatively few studies with modified nucleobases exist. Here we describe the synthesis and hybridization properties of siRNAs bearing size-expanded RNA (xRNA) nucleobases and their use as a novel and systematic set of steric probes in RNAi. xRNA nucleobases are expanded by 2.4 Å using benzo-homologation and retain canonical Watson-Crick base-pairing groups. Our data show that the modified siRNA duplexes display small changes in melting temperature (+1.4 to -5.0 °C); substitutions near the center are somewhat destabilizing to the RNA duplex, while substitutions near the ends are stabilizing. RNAi studies in a dual-reporter luciferase assay in HeLa cells revealed that xRNA nucleobases in the antisense strand reduce activity at some central positions near the seed region but are generally well tolerated near the ends. Most importantly, we observed that xRNA substitutions near the 3'-end increased activity over that of wild-type siRNAs. The data are analyzed in terms of site-dependent steric effects in RISC. Circular dichroism experiments show that single xRNA substitutions do not significantly distort the native A-form helical structure of the siRNA duplex, and serum stability studies demonstrated that xRNA substitutions protect siRNAs against nuclease degradation.

Theoretical study of electron transfer mechanism in biological systems with a QM (MRSCI+DFT)/MM method

Energy Technology Data Exchange (ETDEWEB)

Takada, Toshikazu [Research Program for Computational Science, RIKEN 2-1, Hirosawa, Wako, Saitama 351-0198 (Japan)

2007-07-15

The goal of this project is to understand the charge separation mechanisms in biological systems using the molecular orbital theories. Specially, the charge separation in the photosynthetic reaction center is focused on, since the efficiency in use of the solar energy is extraordinary and the reason for it is still kept unknown. Here, a QM/MM theoretical scheme is employed to take the effects of the surrounding proteins onto the pigments into account. To describe such excited electronic structures, a unified theory by MRSCI and DFT is newly invented. For atoms in the MM space, a new sampling method has also been created, based on the statistical physics. By using these theoretical framework, the excited and positively charged states of the special pair, that is, chlorophyll dimmer are planning to be calculated this year.

Theoretical study of electron transfer mechanism in biological systems with a QM (MRSCI+DFT)/MM method

International Nuclear Information System (INIS)

Takada, Toshikazu

2007-01-01

The goal of this project is to understand the charge separation mechanisms in biological systems using the molecular orbital theories. Specially, the charge separation in the photosynthetic reaction center is focused on, since the efficiency in use of the solar energy is extraordinary and the reason for it is still kept unknown. Here, a QM/MM theoretical scheme is employed to take the effects of the surrounding proteins onto the pigments into account. To describe such excited electronic structures, a unified theory by MRSCI and DFT is newly invented. For atoms in the MM space, a new sampling method has also been created, based on the statistical physics. By using these theoretical framework, the excited and positively charged states of the special pair, that is, chlorophyll dimmer are planning to be calculated this year

The effects of post-treatments and temperature on recovering the methane potential of > 2 mm solid fraction of digested cow manure

DEFF Research Database (Denmark)

Kaparaju, Prasad Laxmi-Narasimha; Rintala, J.A.

2005-01-01

The effects of thermal and chemical treatments, mechanical maceration and freezing and thawing on recovering the remaining methane potential of the > 2 mm solid fraction of digested cow manure - which accounted for 30% of the original potential of digested cow manure - were studied in laboratory...

Steric effects on the primary isotope dependence of secondary kinetic isotope effects in hydride transfer reactions in solution: caused by the isotopically different tunneling ready state conformations?

Science.gov (United States)

Maharjan, Binita; Raghibi Boroujeni, Mahdi; Lefton, Jonathan; White, Ormacinda R; Razzaghi, Mortezaali; Hammann, Blake A; Derakhshani-Molayousefi, Mortaza; Eilers, James E; Lu, Yun

2015-05-27

The observed 1° isotope effect on 2° KIEs in H-transfer reactions has recently been explained on the basis of a H-tunneling mechanism that uses the concept that the tunneling of a heavier isotope requires a shorter donor-acceptor distance (DAD) than that of a lighter isotope. The shorter DAD in D-tunneling, as compared to H-tunneling, could bring about significant spatial crowding effect that stiffens the 2° H/D vibrations, thus decreasing the 2° KIE. This leads to a new physical organic research direction that examines how structure affects the 1° isotope dependence of 2° KIEs and how this dependence provides information about the structure of the tunneling ready states (TRSs). The hypothesis is that H- and D-tunneling have TRS structures which have different DADs, and pronounced 1° isotope effect on 2° KIEs should be observed in tunneling systems that are sterically hindered. This paper investigates the hypothesis by determining the 1° isotope effect on α- and β-2° KIEs for hydride transfer reactions from various hydride donors to different carbocationic hydride acceptors in solution. The systems were designed to include the interactions of the steric groups and the targeted 2° H/D's in the TRSs. The results substantiate our hypothesis, and they are not consistent with the traditional model of H-tunneling and 1°/2° H coupled motions that has been widely used to explain the 1° isotope dependence of 2° KIEs in the enzyme-catalyzed H-transfer reactions. The behaviors of the 1° isotope dependence of 2° KIEs in solution are compared to those with alcohol dehydrogenases, and sources of the observed "puzzling" 2° KIE behaviors in these enzymes are discussed using the concept of the isotopically different TRS conformations.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.

Science.gov (United States)

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik; Harvey, Jeremy N; Mulholland, Adrian J

2016-06-20

The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site, but this is not a prerequisite for reaction via either mechanism. Several active site residues play a role in the binding of mexiletine in the active site, including Thr124 and Phe226. This work reveals key details of the N-hydroxylation of mexiletine and further demonstrates that mechanistic studies using QM/MM methods are useful for understanding drug metabolism.

Opto-mechanical design and development of a 460mm diffractive transmissive telescope

Science.gov (United States)

Qi, Bo; Wang, Lihua; Cui, Zhangang; Bian, Jiang; Xiang, Sihua; Ma, Haotong; Fan, Bin

2018-01-01

Using lightweight, replicated diffractive optics, we can construct extremely large aperture telescopes in space.The transmissive primary significantly reduces the sensitivities to out of plane motion as compared to reflective systems while reducing the manufacturing time and costs. This paper focuses on the design, fabrication and ground demonstration of a 460mm diffractive transmissive telescope the primary F/# is 6, optical field of view is 0.2° imagine bandwidth is 486nm 656nm.The design method of diffractive optical system was verified, the ability to capture a high-quality image using diffractive telescope collection optics was tested.The results show that the limit resolution is 94lp/mm, the diffractive system has a good imagine performance with broad bandwidths. This technology is particularly promising as a means to achieve extremely large optical primaries from compact, lightweight packages.

Mechanical design and fabrication of a prototype undulator for Indus-2

International Nuclear Information System (INIS)

Veerabhadhraiah, T.; Sinha, Gautam; Prabhu, S.S.

2011-01-01

An Apple II type undulator is proposed for 2.5 GeV SRS. For initial studies of magnetic parameters and manufacturing feasibilities, a 6 periods prototype undulator of period length 72 mm and pole gap 20 mm is under development. Mechanical structure with stringent tolerances is required to achieve the required field quality. Stress analysis has been done to study the deflection under the magnetic forces. The prototype structure along with the magnet block holders has been made and mechanical dimensions and geometric tolerances have been measured. In this paper we present the preliminary mechanical design and assembly of static parts of prototype undulator structure. (author)

Synthesis of zinc phthalocyanine with large steric hindrance and its photovoltaic performance for dye-sensitized solar cells.

Science.gov (United States)

Lin, Li; Peng, Bosi; Shi, Wenye; Guo, Yingying; Li, Renjie

2015-03-28

A zinc phthalocyanine (ZnPc) derivative (Zn-tri-PcNc-8) containing tri-benzonaphtho-condensed porphyrazine with one carboxylic and six diphenylphenoxy peripheral substitutions was designed and synthesized as a sensitizer for dye-sensitized solar cells (DSSCs). For the purpose of extending the absorption spectra while minimizing the formation of ZnPc molecular aggregates, bulky 2,6-diphenylphenoxy groups were used as electron donor moieties, and the carboxylic group as an anchoring group to graft the sensitizer onto the semiconductor. It was found that a TiO2-based solar cell sensitized by Zn-tri-PcNc-8 shows a maximum incident photon-to-current conversion efficiency in the red/near-IR light range (650-750 nm), and a solar cell sensitized at near room temperature (30 °C) for 48 h exhibits the best efficiency (3.01%). The efficiency was much higher than that (1.96%) for a solar cell sensitized by its analogue (Zn-tri-PcNc-2) having one carboxyl and three tert-butyl groups without chenodeoxycholic acid (CDCA), indicating that the introduction of six bulky diphenylphenoxy substitutions with large steric hindrance in the ZnPc macrocycle can effectively suppress the molecular aggregates, thus resulting in an improved conversion efficiency. The present results shed light on an effective solution to adjust the ZnPc property via chemical modification such as changing the "push-pull" effect and adding large steric hindrance substituents to further improve the efficiency of the phthalocyanine-sensitized solar cell.

Structural plasticity mediates distinct GAP-dependent GTP hydrolysis mechanisms in Rab33 and Rab5.

Science.gov (United States)

Majumdar, Soneya; Acharya, Abhishek; Prakash, Balaji

2017-12-01

The classical GTP hydrolysis mechanism, as seen in Ras, employs a catalytic glutamine provided in cis by the GTPase and an arginine supplied in trans by a GTPase activating protein (GAP). The key idea emergent from a large body of research on small GTPases is that GTPases employ a variety of different hydrolysis mechanisms; evidently, these variations permit diverse rates of GTPase inactivation, crucial for temporal regulation of different biological processes. Recently, we unified these variations and argued that a steric clash between active site residues (corresponding to positions 12 and 61 of Ras) governs whether a GTPase utilizes the cis-Gln or the trans-Gln (from the GAP) for catalysis. As the cis-Gln encounters a steric clash, the Rab GTPases employ the so-called dual finger mechanism where the interacting GAP supplies a trans-Gln for catalysis. Using experimental and computational methods, we demonstrate how the cis-Gln of Rab33 overcomes the steric clash when it is stabilized by a residue in the vicinity. In effect, this demonstrates how both cis-Gln- and trans-Gln-mediated mechanisms could operate in the same GTPase in different contexts, i.e. depending on the GAP that regulates its action. Interestingly, in the case of Rab5, which possesses a higher intrinsic GTP hydrolysis rate, a similar stabilization of the cis-Gln appears to overcome the steric clash. Taken together with the mechanisms seen for Rab1, it is evident that the observed variations in Rab and their GAP partners allow structural plasticity, or in other words, the choice of different catalytic mechanisms. © 2017 Federation of European Biochemical Societies.

Sterics level the rates of proton transfer to [Ni(XPh){PhP(CH₂CH₂PPh₂)₂}]⁺ (X = O, S or Se).

Science.gov (United States)

Alwaaly, Ahmed; Henderson, Richard A

2014-09-04

Rates of proton transfers between lutH(+) (lut = 2,6-dimethylpyridine) and [Ni(XPh)(PhP{CH2CH2PPh2}2)](+) (X = O, S or Se) are slow and show little variation (k(O) : k(S) : k(Se) = 1 : 12 : 9). This unusual behaviour is a consequence of sterics affecting the optimal interaction between the reactants prior to proton transfer.

Structural-performance testing of titanium-shell lead-matrix container MM2

Energy Technology Data Exchange (ETDEWEB)

Hosaluk, L. J.; Barrie, J. N.

1992-05-15

This report describes the hydrostatic structural-performance testing of a half-scale, titanium-shell, lead-matrix container (MM2) with a large, simulated volumetric casting defect. Mechancial behaviour of the container is assessed from extensive surface-strain measurements and post-test non-destructive and destructive examinations. Measured strain data are compared briefly with analytical results from a finite-element model of a previous test prototype, MM1, and with data generated by a finite-difference computer code. Finally, procedures are recommended for more detailed analytical modelling. (auth)

QM/MM free energy simulations: recent progress and challenges

Science.gov (United States)

Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor

2016-01-01

Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170

MM2-thalamic Creutzfeldt-Jakob disease: neuropathological, biochemical and transmission studies identify a distinctive prion strain.

Science.gov (United States)

Moda, Fabio; Suardi, Silvia; Di Fede, Giuseppe; Indaco, Antonio; Limido, Lucia; Vimercati, Chiara; Ruggerone, Margherita; Campagnani, Ilaria; Langeveld, Jan; Terruzzi, Alessandro; Brambilla, Antonio; Zerbi, Pietro; Fociani, Paolo; Bishop, Matthew T; Will, Robert G; Manson, Jean C; Giaccone, Giorgio; Tagliavini, Fabrizio

2012-09-01

In Creutzfeldt-Jakob disease (CJD), molecular typing based on the size of the protease resistant core of the disease-associated prion protein (PrP(Sc) ) and the M/V polymorphism at codon 129 of the PRNP gene correlates with the clinico-pathologic subtypes. Approximately 95% of the sporadic 129MM CJD patients are characterized by cerebral deposition of type 1 PrP(Sc) and correspond to the classic clinical CJD phenotype. The rare 129MM CJD patients with type 2 PrP(Sc) are further subdivided in a cortical and a thalamic form also indicated as sporadic fatal insomnia. We observed two young patients with MM2-thalamic CJD. Main neuropathological features were diffuse, synaptic PrP immunoreactivity in the cerebral cortex and severe neuronal loss and gliosis in the thalamus and olivary nucleus. Western blot analysis showed the presence of type 2A PrP(Sc) . Challenge of transgenic mice expressing 129MM human PrP showed that MM2-thalamic sporadic CJD (sCJD) was able to transmit the disease, at variance with MM2-cortical sCJD. The affected mice showed deposition of type 2A PrP(Sc) , a scenario that is unprecedented in this mouse line. These data indicate that MM2-thalamic sCJD is caused by a prion strain distinct from the other sCJD subtypes including the MM2-cortical form. © 2012 The Authors; Brain Pathology © 2012 International Society of Neuropathology.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

Science.gov (United States)

Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-01-17

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4 O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S 1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal

Comparison between 4.0-mm stainless steel and 4.75-mm titanium alloy single-rod spinal instrumentation for anterior thoracoscopic scoliosis surgery.

Science.gov (United States)

Yoon, Seung Hwan; Ugrinow, Valerie L; Upasani, Vidyadhar V; Pawelek, Jeff B; Newton, Peter O

2008-09-15

deformity correction at 2-years postop and a lower incidence of instrumentation-related complications (pseudarthrosis, rod breakage, and surgical revisions) compared to the 4.0-mm stainless steel construct. Improved outcomes with the titanium alloy construct are likely because of the mechanical properties of the implant, refined patient selection criteria, and greater surgical experience gained with time.

SSC 40 mm cable results and 50 mm design discussions

International Nuclear Information System (INIS)

Christopherson, D.; Capone, D.; Hannaford, R.; Remsbottom, R.; Jayakumar, R.; Snitchler, G.; Scanlan, R.; Royet, J.

1990-09-01

A summary of the cable produced for the 1990 40 mm Dipole Program is presented. The cable design parameters for the 50 mm Dipole Program are discussed, as well as portions of the SSC specification draft. Considerations leading to the final cable configuration and the results of preliminary trials are included. The first iteration of a strand mapping program to automate cable strand maps is introduced. 7 refs., 2 figs., 1 tab

Development and application of QM/MM methods to study the solvation effects and surfaces

Energy Technology Data Exchange (ETDEWEB)

Dibya, Pooja Arora [Iowa State Univ., Ames, IA (United States)

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize the computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work

Electrical behaviour of heterobimetallic [MM'(EtCS2)4] (MM'=NiPd, NiPt, PdPt) and MM'X-chain polymers [PtM(EtCS2)4I] (M=Ni, Pd).

Science.gov (United States)

Givaja, Gonzalo; Castillo, Oscar; Mateo, Eva; Gallego, Almudena; Gómez-García, Carlos J; Calzolari, Arrigo; di Felice, Rosa; Zamora, Félix

2012-11-26

Herein, we report the isolation of new heterobimetallic complexes [Ni(0.6)Pd(1.4)(EtCS(2))(4)] (1), [NiPt(EtCS(2))(4)] (2) and [Pd(0.4)Pt(1.6)(EtCS(2))(4)] (3), which were constructed by using transmetallation procedures. Subsequent oxidation with iodine furnished the MM'X monodimensional chains [Ni(0.6)Pt(1.4)(EtCS(2))(4)I] (4) and [Ni(0.1)Pd(0.3)Pt(1.6)(EtCS(2))(4)I] (5). The physical properties of these systems were investigated and the chain structures 4 and 5 were found to be reminiscent of the parent [Pt(2)(EtCS(2))(4)I] species. However, they were more sensitively dependent on the localised nature of the charge on the Ni ion, which caused spontaneous breaking of the conduction bands. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and structural characterization of PHP[(C(5)Me(4))(2)], a monodentate chiral phosphine derived from intramolecular C-C coupling of tetramethylcyclopentadienyl groups: an evaluation of steric and electronic properties.

Science.gov (United States)

Shin, J H; Bridgewater, B M; Churchill, D G; Parkin, G

2001-10-22

The chiral monodentate phosphine PhP[(C(5)Me(4))(2)] is readily obtained by oxidation of the lithium complex Li(2)[PhP(C(5)Me(4))(2)] with I(2), which couples the two cyclopentadienyl groups to form a five-membered heterocyclic ring. The steric and electronic properties of PhP[(C(5)Me(4))(2)] have been evaluated by X-ray diffraction and IR spectroscopic studies on a variety of derivatives, including Ph[(C(5)Me(4))(2)]PE (E = S, Se), Cp*MCl(4)[P[(C(5)Me(4))(2)]Ph] (M = Mo, Ta), Ir[P[(C(5)Me(4))(2)]Ph](2)(CO)Cl, and CpFe(CO)[PhP[(C(5)Me(4))(2)

Micro-flow synthesis and structural analysis of sterically crowded diimine ligands with five aryl rings

Directory of Open Access Journals (Sweden)

Shinichiro Fuse

2013-11-01

Full Text Available Sterically crowded diimine ligands with five aryl rings were prepared in one step in good yields using a micro-flow technique. X-ray crystallographic analysis revealed the detailed structure of the bulky ligands. The nickel complexes prepared from the ligands exerted high polymerization activity in the ethylene homopolymerization and copolymerization of ethylene with polar monomers.

Mathematical model of mechanical testing of bone-implant (4.5 mm LCP construct

Directory of Open Access Journals (Sweden)

Lucie Urbanová

2012-01-01

Full Text Available The study deals with the possibility of substituting time- and material-demanding mechanical testing of a bone defect fixation by mathematical modelling. Based on the mechanical model, a mathematical model of bone-implant construct stabilizing experimental segmental femoral bone defect (segmental ostectomy in a miniature pig ex vivo model using 4.5 mm titanium LCP was created. It was subsequently computer-loaded by forces acting parallel to the long axis of the construct. By the effect of the acting forces the displacement vector sum of individual construct points occurred. The greatest displacement was noted in the end segments of the bone in close proximity to ostectomy and in the area of the empty central plate hole (without screw at the level of the segmental bone defect. By studying the equivalent von Mises stress σEQV on LCP as part of the tested construct we found that the greatest changes of stress occur in the place of the empty central plate hole. The distribution of this strain was relatively symmetrical along both sides of the hole. The exceeding of the yield stress value and irreversible plastic deformations in this segment of LCP occurred at the acting of the force of 360 N. These findings are in line with the character of damage of the same construct loaded during its mechanic testing. We succeeded in creating a mathematical model of the bone-implant construct which may be further used for computer modelling of real loading of similar constructs chosen for fixation of bone defects in both experimental and clinical practice.

Multifaceted catalytic hydrogenation of amides via diverse activation of a sterically confined bipyridine-ruthenium framework.

Science.gov (United States)

Miura, Takashi; Naruto, Masayuki; Toda, Katsuaki; Shimomura, Taiki; Saito, Susumu

2017-05-16

Amides are ubiquitous and abundant in nature and our society, but are very stable and reluctant to salt-free, catalytic chemical transformations. Through the activation of a "sterically confined bipyridine-ruthenium (Ru) framework (molecularly well-designed site to confine adsorbed H 2 in)" of a precatalyst, catalytic hydrogenation of formamides through polyamide is achieved under a wide range of reaction conditions. Both C=O bond and C-N bond cleavage of a lactam became also possible using a single precatalyst. That is, catalyst diversity is induced by activation and stepwise multiple hydrogenation of a single precatalyst when the conditions are varied. The versatile catalysts have different structures and different resting states for multifaceted amide hydrogenation, but the common structure produced upon reaction with H 2 , which catalyzes hydrogenation, seems to be "H-Ru-N-H."

Mechanical stability assessment of novel orthodontic mini-implant designs: Part 2.

Science.gov (United States)

Hong, Christine; Truong, Peter; Song, Ha Na; Wu, Benjamin M; Moon, Won

2011-11-01

To assess the mechanical stability of a newly revised orthodontic mini-implant design (N2) compared with a design introduced in Part 1 of the study (N1) and the most widely-used commercially-available design (CA). To evaluate the mean buccal bone thickness of maxillary and mandibular posterior teeth using cone-beam computed tomography (CBCT). From the CBCT scans of 20 patients, six tomographic cross-sections were generated for each tooth. Buccal bone thickness was measured from the most convex point on the bone to the root surface. CA (1.5 mm in diameter and 6 mm in length), N1, and N2 (shorter and narrower than N1) were inserted in simulated bone with cortical and trabecular bone layers. Mechanical stability was compared in vitro through torque and lateral displacement tests. The bone thickness ranged from 2.26 to 3.88 mm. Maximum insertion torque was decreased significantly in N2 compared to N1. However, force levels for all displacement distances and torque ratio were the highest in N2, followed by N1 and CA (α = .05). Both torque and lateral displacement tests highlighted the enhanced stability of N2 compared with CA. Design revisions to N1 effectively mitigated N1's high insertion torque and thus potentially reduced microdamage to the surrounding bone. The N2 design is promising as evidenced by enhanced stability and high mechanical efficiency. Moreover, N2 is not limited to placement in interradicular spaces and has the capacity to be placed in the buccal bone superficial to the root surface with diminished risk of endangering nearby anatomic structures during placement and treatment.

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective.

Science.gov (United States)

Maxwell, Peter I; Popelier, Paul L A

2017-11-05

Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (O i -1 , C i , N i , N i +1 ) and some sidechain hydrogen atoms (H γ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the O i -1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Structure and dynamics of a [1:1] drug-DNA complex: Analysis of 2D NMR data using molecular mechanics and molecular dynamics calculations

International Nuclear Information System (INIS)

Sarma, R.H.; Sarma, M.H.; Umemoto, K.

1990-01-01

1D/2D NMR studies are reported for a [1:1] complex of d(GA 4 T 4 C) 2 and Dst2 (an analogue of distamycin A). Full- Matrix NOESY Simulations, Molecular Mechanics and Molecular Dynamics Calculations are performed to analyze the NMR data. Results show that drug-DNA complex formation is driven by static features like H-bonding and steric interactions in the minor-groove of DNA. As a consequence of drug binding, a non-linear oscillatory mode is activated. In this mode the molecule samples equilibrium structural states of difference degrees of bending. It is noted that these structures belong to three distinctly different energy wells that satisfy the same NMR data. 14 refs., 4 figs., 2 tabs

Steric-electronic effects in malarial peptides inducing sterile immunity

Energy Technology Data Exchange (ETDEWEB)

Moreno-Vranich, Armando [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Patarroyo, Manuel E., E-mail: mepatarr@mail.com [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Universidad Nacional de Colombia, Bogota (Colombia)

2012-07-13

Highlights: Black-Right-Pointing-Pointer Is it evident that the residues position are relevant regarding of {phi} angular value. Black-Right-Pointing-Pointer The geometry considered for detailing the alterations undergone by HABPs. Black-Right-Pointing-Pointer The inter planar interactions ruled by clashes between the atoms making them up. -- Abstract: Conserved Plasmodium falciparum high activity binding peptides' (HABPs) most relevant proteins involved in malaria parasite invasion are immunologically silent; critical binding residues must therefore be specifically replaced to render them highly immunogenic and protection-inducing. Such changes have a tremendous impact on these peptides' steric-electronic effects, such as modifications to peptide length peptide bonds and electronic orbitals' disposition, to allow a better fit into immune system MHCII molecules and better interaction with the TCR which might account for the final immunological outcome.

Intravascular ultrasonic-photoacoustic (IVUP) endoscope with 2.2-mm diameter catheter for medical imaging.

Science.gov (United States)

Bui, Nhat Quang; Hlaing, Kyu Kyu; Nguyen, Van Phuc; Nguyen, Trung Hau; Oh, Yun-Ok; Fan, Xiao Feng; Lee, Yong Wook; Nam, Seung Yun; Kang, Hyun Wook; Oh, Junghwan

2015-10-01

Intravascular ultrasound (IVUS) imaging is extremely important for detection and characterization of high-risk atherosclerotic plaques as well as gastrointestinal diseases. Recently, intravascular photoacoustic (IVPA) imaging has been used to differentiate the composition of biological tissues with high optical contrast and ultrasonic resolution. The combination of these imaging techniques could provide morphological information and molecular screening to characterize abnormal tissues, which would help physicians to ensure vital therapeutic value and prognostic significance for patients before commencing therapy. In this study, integration of a high-frequency IVUS imaging catheter (45MHz, single-element, unfocused, 0.7mm in diameter) with a multi-mode optical fiber (0.6mm in core diameter, 0.22 NA), an integrated intravascular ultrasonic-photoacoustic (IVUP) imaging catheter, was developed to provide spatial and functional information on light distribution in a turbid sample. Simultaneously, IVUS imaging was co-registered to IVPA imaging to construct 3D volumetric sample images. In a phantom study, a polyvinyl alcohol (PVA) tissue-mimicking arterial vessel phantom with indocyanine green (ICG) and methylene blue (MB) inclusion was used to demonstrate the feasibility of mapping the biological dyes, which are used in cardiovascular and cancer diagnostics. For the ex vivo study, an excised sample of pig intestine with ICG was utilized to target the biomarkers present in the gastrointestinal tumors or the atherosclerotic plaques with the proposed hybrid technique. The results indicated that IVUP endoscope with the 2.2-mm diameter catheter could be a useful tool for medical imaging. Copyright © 2015 Elsevier Ltd. All rights reserved.

Targeted Sterically Stabilized Phospholipid siRNA Nanomedicine for Hepatic and Renal Fibrosis

Directory of Open Access Journals (Sweden)

Fatima Khaja

2016-01-01

Full Text Available Since its discovery, small interfering RNA (siRNA has been considered a potent tool for modulating gene expression. It has the ability to specifically target proteins via selective degradation of messenger RNA (mRNA not easily accessed by conventional drugs. Hence, RNA interference (RNAi therapeutics have great potential in the treatment of many diseases caused by faulty protein expression such as fibrosis and cancer. However, for clinical application siRNA faces a number of obstacles, such as poor in vivo stability, and off-target effects. Here we developed a unique targeted nanomedicine to tackle current siRNA delivery issues by formulating a biocompatible, biodegradable and relatively inexpensive nanocarrier of sterically stabilized phospholipid nanoparticles (SSLNPs. This nanocarrier is capable of incorporating siRNA in its core through self-association with a novel cationic lipid composed of naturally occuring phospholipids and amino acids. This overall assembly protects and delivers sufficient amounts of siRNA to knockdown over-expressed protein in target cells. The siRNA used in this study, targets connective tissue growth factor (CTGF, an important regulator of fibrosis in both hepatic and renal cells. Furthermore, asialoglycoprotein receptors are targeted by attaching the galactosamine ligand to the nanocarries which enhances the uptake of nanoparticles by hepatocytes and renal tubular epithelial cells, the major producers of CTGF in fibrosis. On animals this innovative nanoconstruct, small interfering RNA in sterically stabilized phospholipid nanoparticles (siRNA-SSLNP, showed favorable pharmacokinetic properties and accumulated mostly in hepatic and renal tissues making siRNA-SSLNP a suitable system for targeting liver and kidney fibrotic diseases.

The role of PEG conformation in mixed layers: from protein corona substrate to steric stabilization avoiding protein adsorption

Directory of Open Access Journals (Sweden)

Joan Comenge

2015-03-01

Full Text Available Although nanoparticles (NPs have been traditionally modified with a single ligand layer, mixture of ligands might help to combine different functionalities and to further engineer the NP surface. A detailed study of the competition between an alkanethiol (11-mercaptoundecanoic acid and SH-PEG for the surface of AuNPs and the resultant behaviors of this model nanoconjugate is presented here. As a result, the physicochemical properties of these conjugates can be progressively tuned by controlling the composition and especially the conformation of the mixed monolayer. This has implications in the physiological stability. The controlled changes on the SH-PEG conformation rather than its concentration induce a change in the stabilization mechanism from electrostatic repulsion to steric hindrance, which changes the biological fate of NPs. Importantly, the adsorption of proteins on the conjugates can be tailored by tuning the composition and conformation of the mixed layer.

On the difference between additive and subtractive QM/MM calculations

Science.gov (United States)

Cao, Lili; Ryde, Ulf

2018-04-01

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e. the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.

On the Difference Between Additive and Subtractive QM/MM Calculations

Directory of Open Access Journals (Sweden)

Lili Cao

2018-04-01

Full Text Available The combined quantum mechanical (QM and molecular mechanical (MM approach (QM/MM is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.

PI-RADS version 2: evaluation of diffusion-weighted imaging interpretation between b = 1000 and b = 1500 s mm-2.

Science.gov (United States)

Kwon, Mi-Ri; Kim, Chan Kyo; Kim, Jae-Hun

2017-11-01

To investigate the variability of diffusion-weighted imaging (DWI) interpretation of Prostate Imaging Reporting and Data System (PI-RADS) version 2 (v2) in evaluating prostate cancer (PCa). 154 patients with PCa underwent multiparametric 3T MRI, followed by radical prostatectomy. DWI with different b values (b = 0, 100, 1000 and 1500 s mm - 2 ) was obtained. Using the PI-RADS v2, two radiologists independently scored suspicious lesions in each patient and compared DWI of b = 1000 (DWI 1000 ) with 1500 (DWI 1500 ) s mm - 2 . On DWI 1000 and DWI 1500 , the intermethod and interobserver agreements of DWI scores were excellent in all patients (κ ≥ 0.873). In each peripheral zone and transition zone DWI scores, both observers showed excellent intermethod agreement between DWI 1000 and DWI 1500 (κ ≥ 0.897), and interobserver agreement for DWI 1000 and DWI 1500 was good to excellent (κ ≥ 0.796). For estimating clinically significant cancer, the area under receiver operating characteristics curves of DWI 1000 and DWI 1500 were 0.710 and 0.724 for observer 1 (p = 0.11), and 0.649 and 0.656 for observer 2 (p = 0.12), respectively. The PI-RADS v2 scoring at 3T shows excellent agreement between DWI 1000 and DWI 1500 in evaluating PCa, with excellent inter-observer agreement. Advance in knowledge: DWI using b = 1000 s mm -2 instead of b = 1500 s mm -2 reduces examination time or image distortion, with improved the signal-to-noise ratio.

Steric control of redox events in organo-uranium chemistry: synthesis and characterisation of U(V) oxo and nitrido complexes

OpenAIRE

Tsoureas, Nikolaos; Kilpatrick, Alexander; Inman, Christopher; Cloke, Frederick Geoffrey

2016-01-01

The synthesis and molecular structures of a U(V) neutral terminal oxo complex and a U(V) sodium uranium nitride contact ion pair are described. The synthesis of the former is achieved by the use of tBuNCO as a mild oxygen transfer reagent, whilst that of the latter is via the reduction of NaN3. Both mono-uranium complexes are stabilised by the presence of bulky silyl substituents on the ligand framework that facilitate a 2e- oxidation of a single U(III) centre. In contrast, when steric hindra...

A 2.5-mm diameter probe for photoacoustic and ultrasonic endoscopy.

Science.gov (United States)

Yang, Joon-Mo; Chen, Ruimin; Favazza, Christopher; Yao, Junjie; Li, Chiye; Hu, Zhilin; Zhou, Qifa; Shung, K Kirk; Wang, Lihong V

2012-10-08

We have created a 2.5-mm outer diameter integrated photo-acoustic and ultrasonic mini-probe which can be inserted into a standard video endoscope's instrument channel. A small-diameter focused ultrasonic transducer made of PMN-PT provides adequate signal sensitivity, and enables miniaturization of the probe. Additionally, this new endoscopic probe utilizes the same scanning mirror and micromotor-based built-in actuator described in our previous reports; however, the length of the rigid distal section of the new probe has been further reduced to ~35 mm. This paper describes the technical details of the mini-probe and presents experimental results that both quantify the imaging performance and demonstrate its in vivo imaging capability, which suggests that it could work as a mini-probe for certain clinical applications.

A 2.5-mm diameter probe for photoacoustic and ultrasonic endoscopy

Science.gov (United States)

Yang, Joon-Mo; Chen, Ruimin; Favazza, Christopher; Yao, Junjie; Li, Chiye; Hu, Zhilin; Zhou, Qifa; Shung, K. Kirk; Wang, Lihong V.

2012-01-01

We have created a 2.5-mm outer diameter integrated photo-acoustic and ultrasonic mini-probe which can be inserted into a standard video endoscope’s instrument channel. A small-diameter focused ultrasonic transducer made of PMN-PT provides adequate signal sensitivity, and enables miniaturization of the probe. Additionally, this new endoscopic probe utilizes the same scanning mirror and micromotor-based built-in actuator described in our previous reports; however, the length of the rigid distal section of the new probe has been further reduced to ~35 mm. This paper describes the technical details of the mini-probe and presents experimental results that both quantify the imaging performance and demonstrate its in vivo imaging capability, which suggests that it could work as a mini-probe for certain clinical applications. PMID:23188360

Application of Computational Methods Mm2 and Gussian for Studing Unimolecular Decomposition of Vinil Ethers based on the Mechanism of Hydrogen Bonding

OpenAIRE

Behnaz Shahrokh; Garnik N. Sargsyan; Arkadi B. Harutyunyan

2012-01-01

Investigations of the unimolecular decomposition of vinyl ethyl ether (VEE), vinyl propyl ether (VPE) and vinyl butyl ether (VBE) have shown that activation of the molecule of a ether results in formation of a cyclic construction - the transition state (TS), which may lead to the displacement of the thermodynamic equilibrium towards the reaction products. The TS is obtained by applying energy minimization relative to the ground state of an ether under the program MM2 when...

Different mechanisms are involved in the antibody mediated inhibition of ligand binding to the urokinase receptor

DEFF Research Database (Denmark)

List, K; Høyer-Hansen, G; Rønne, E

1999-01-01

Certain monoclonal antibodies are capable of inhibiting the biological binding reactions of their target proteins. At the molecular level, this type of effect may be brought about by completely different mechanisms, such as competition for common binding determinants, steric hindrance or interfer......Certain monoclonal antibodies are capable of inhibiting the biological binding reactions of their target proteins. At the molecular level, this type of effect may be brought about by completely different mechanisms, such as competition for common binding determinants, steric hindrance......) can be employed as a highly useful tool to characterize the inhibitory mechanism of specific antagonist antibodies. Two inhibitory antibodies against uPAR, mAb R3 and mAb R5, were shown to exhibit competitive and non-competitive inhibition, respectively, of ligand binding to the receptor. The former...

Fourier transform infrared absorption spectroscopy characterization of gaseous atmospheric pressure plasmas with 2 mm spatial resolution

Energy Technology Data Exchange (ETDEWEB)

Laroche, G. [Laboratoire d' Ingenierie de Surface, Centre de Recherche sur les Materiaux Avances, Departement de genie des mines, de la metallurgie et des materiaux, Universite Laval, 1065, avenue de la Medecine, Quebec G1V 0A6 (Canada); Centre de recherche du CHUQ, Hopital St Francois d' Assise, 10, rue de l' Espinay, local E0-165, Quebec G1L 3L5 (Canada); Vallade, J. [Laboratoire Procedes, Materiaux et Energie Solaire, PROMES, CNRS, Technosud, Rambla de la Thermodynamique, F-66100 Perpignan (France); Agence de l' environnement et de la Ma Latin-Small-Letter-Dotless-I -carettrise de l' Energie, 20, avenue du Gresille, BP 90406, F-49004 Angers Cedex 01 (France); Bazinette, R.; Hernandez, E.; Hernandez, G.; Massines, F. [Laboratoire Procedes, Materiaux et Energie Solaire, PROMES, CNRS, Technosud, Rambla de la Thermodynamique, F-66100 Perpignan (France); Nijnatten, P. van [OMT Solutions bv, High Tech Campus 9, 5656AE Eindhoven (Netherlands)

2012-10-15

This paper describes an optical setup built to record Fourier transform infrared (FTIR) absorption spectra in an atmospheric pressure plasma with a spatial resolution of 2 mm. The overall system consisted of three basic parts: (1) optical components located within the FTIR sample compartment, making it possible to define the size of the infrared beam (2 mm Multiplication-Sign 2 mm over a path length of 50 mm) imaged at the site of the plasma by (2) an optical interface positioned between the spectrometer and the plasma reactor. Once through the plasma region, (3) a retro-reflector module, located behind the plasma reactor, redirected the infrared beam coincident to the incident path up to a 45 Degree-Sign beamsplitter to reflect the beam toward a narrow-band mercury-cadmium-telluride detector. The antireflective plasma-coating experiments performed with ammonia and silane demonstrated that it was possible to quantify 42 and 2 ppm of these species in argon, respectively. In the case of ammonia, this was approximately three times less than this gas concentration typically used in plasma coating experiments while the silane limit of quantification was 35 times lower. Moreover, 70% of the incoming infrared radiation was focused within a 2 mm width at the site of the plasma, in reasonable agreement with the expected spatial resolution. The possibility of reaching this spatial resolution thus enabled us to measure the gaseous precursor consumption as a function of their residence time in the plasma.

Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug-Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies.

Science.gov (United States)

Yao, Jianzhuang; Wang, Xia; Luo, Haixia; Gu, Pengfei

2017-11-16

Shikimate kinase (SK) is the fifth bacterial enzyme involved in the shikimate pathway for biosynthesis of life-indispensable components, such as aromatic amino acids. The absence of the shikimate pathway in humans makes SK an attractive target for the rational design of drugs aimed at pathogenesis bacteria, such as Mycobacterium tuberculosis and Helicobacter pylori. However, an effective inhibitor of SK (e.g., a transition-state analogue) is still not available on the market due, at least in part, to a lack of knowledge on the catalytic mechanism and the nature of the rate-limiting transition state. Herein, quantum mechanical/molecular mechanical (QM/MM) reaction coordinate, molecular dynamics (MD), and free-energy simulations have been performed to answer these questions. The results presented herein demonstrate that the phosphoryl-transfer process, which is the rate-limiting step of SK-catalyzed phosphorylation of shikimic acid (SKM), is a concerted one-step reaction proceeding through a loose transition state. The computational results agree well with those of experimental studies, specifically NMR results, X-ray crystal structure observation, and activation free-energy barrier. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of 2 mm thin-slice scanning with bone algorithm on conventional CT in diagnosis of the pulmonary diseases

International Nuclear Information System (INIS)

Zhang Xianheng; Li Xiuhua; Wang Fenghua

2004-01-01

Objective: To evaluate the value of 2 mm thin-slice conventional CT scan with bone algorithm in diagnosis and differential diagnosis in the pulmonary diseases. Methods: In total 135 cases of the pulmonary diseases were routinely scanned by conventional scan, 10 mm per slice, with standard algorithm, then the 2 mm thin-slice scan with bone algorithm was performed at the interested region of the lungs. Result: According to the comparative study of the CT signs between 10 mm slice scan with standard algorithm and 2 mm thin-slice scan with bone algorithm, the latter was better on displaying the pulmonary axial interstium, intralobular septum, subpleura lines, honeycombing, 2-5 mm nodulars and anomalies of bronchial wall. Conclusion: According to the study of 135 cases, 2 mm thin-slice scan with bone algorithm is superior to 10 mm slice scan with standard algorithm in demonstrating the pulmonary lesions. It has a similar value with high-resolution spiral CT in the diagnosis of the pulmonary solitary or diffuse nodules, pulmonary diffuse interstitial lesions and the lesions of the airway. It is practical and advisable in the community hospital

Evolution from S3 to S4 States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics.

Science.gov (United States)

Narzi, Daniele; Capone, Matteo; Bovi, Daniele; Guidoni, Leonardo

2018-04-16

Water oxidation in the early steps of natural photosynthesis is fulfilled by photosystem II, which is a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of photosystem II, which consists of a Mn4Ca metal cluster, at which, after the accumulation of four oxidising equivalents through five steps (S0-S4) of the Kok-Joliot cycle, two water molecules are split into electrons, protons, and molecular oxygen. In recent years, by combining experimental and theoretical approaches, new insights have been achieved into the structural and electronic properties of different steps of the catalytic cycle. Nevertheless, the exact catalytic mechanism, especially concerning the final stages of the cycle, remains elusive and greatly debated. Herein, by means of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, from the structural, electronic, and magnetic points of view, the S 3 state before and upon oxidation has been characterised. In contrast with the S 2 state, the oxidation of the S 3 state is not followed by a spontaneous proton-coupled electron-transfer event. Nevertheless, upon modelling the reduction of the tyrosine residue in photosystem II (Tyr Z ) and the protonation of Asp61, spontaneous proton transfer occurs, leading to the deprotonation of an oxygen atom bound to Mn1; thus making it available for O-O bond formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

QM/MM studies on the excited-state relaxation mechanism of a semisynthetic dTPT3 base.

Science.gov (United States)

Guo, Wei-Wei; Zhang, Teng-Shuo; Fang, Wei-Hai; Cui, Ganglong

2018-02-14

Semisynthetic alphabets can potentially increase the genetic information stored in DNA through the formation of unusual base pairs. Recent experiments have shown that near-visible-light irradiation of the dTPT3 chromophore could lead to the formation of a reactive triplet state and of singlet oxygen in high quantum yields. However, the detailed excited-state relaxation paths that populate the lowest triplet state are unclear. Herein, we have for the first time employed the QM(MS-CASPT2//CASSCF)/MM method to explore the spectroscopic properties and excited-state relaxation mechanism of the aqueous dTPT3 chromophore. On the basis of the results, we have found that (1) the S 2 ( 1 ππ*) state of dTPT3 is the initially populated excited singlet state upon near-visible light irradiation; and (2) there are two efficient relaxation pathways to populate the lowest triplet state, i.e. T 1 ( 3 ππ*). In the first one, the S 2 ( 1 ππ*) system first decays to the S 1 ( 1 nπ*) state near the S 2 /S 1 conical intersection, which is followed by an efficient S 1 → T 1 intersystem crossing process at the S 1 /T 1 crossing point; in the second one, an efficient S 2 → T 2 intersystem crossing takes place first, and then, the T 2 ( 3 nπ*) system hops to the T 1 ( 3 ππ*) state through an internal conversion process at the T 2 /T 1 conical intersection. Moreover, an S 2 /S 1 /T 2 intersection region is found to play a vital role in the excited-state relaxation. These new mechanistic insights help in understanding the photophysics and photochemistry of unusual base pairs.

Effects of heat input on mechanical properties of metal inert gas welded 1.6 mm thick galvanized steel sheet

International Nuclear Information System (INIS)

Rafiqul, M I; Ishak, M; Rahman, M M

2012-01-01

It is usually a lot easier and less expensive to galvanize steel before it is welded into useful products. Galvanizing afterwards is almost impossible. In this research work, Galvanized Steel was welded by using the ER 308L stainless steel filler material. This work was done to find out an alternative way of welding and investigate the effects of heat input on the mechanical properties of butt welded joints of Galvanized Steel. A 13.7 kW maximum capacity MIG welding machine was used to join 1.6 mm thick sheet of galvanized steel with V groove and no gap between mm. Heat inputs was gradually increased from 21.06 to 25.07 joules/mm in this study. The result shows almost macro defects free welding and with increasing heat input the ultimate tensile strength and welding efficiency decrease. The Vickers hardness also decreases at HAZ with increasing heat input and for each individual specimen; hardness was lowest in heat affected zone (HAZ), intermediate in base metal and maximum in welded zone. The fracture for all specimens was in the heat affected zone while testing in the universal testing machine.

Effects of heat input on mechanical properties of metal inert gas welded 1.6 mm thick galvanized steel sheet

Science.gov (United States)

Rafiqul, M. I.; Ishak, M.; Rahman, M. M.

2012-09-01

It is usually a lot easier and less expensive to galvanize steel before it is welded into useful products. Galvanizing afterwards is almost impossible. In this research work, Galvanized Steel was welded by using the ER 308L stainless steel filler material. This work was done to find out an alternative way of welding and investigate the effects of heat input on the mechanical properties of butt welded joints of Galvanized Steel. A 13.7 kW maximum capacity MIG welding machine was used to join 1.6 mm thick sheet of galvanized steel with V groove and no gap between mm. Heat inputs was gradually increased from 21.06 to 25.07 joules/mm in this study. The result shows almost macro defects free welding and with increasing heat input the ultimate tensile strength and welding efficiency decrease. The Vickers hardness also decreases at HAZ with increasing heat input and for each individual specimen; hardness was lowest in heat affected zone (HAZ), intermediate in base metal and maximum in welded zone. The fracture for all specimens was in the heat affected zone while testing in the universal testing machine.

QM/MM-MD simulations of conjugated polyelectrolytes

DEFF Research Database (Denmark)

Sjöqvist, Jonas; Linares, Mathieu; Mikkelsen, Kurt Valentin

2014-01-01

A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field desc...

Modulation of erythrocyte membrane mechanical stability by 2,3-diphosphoglycerate in the neonatal poikilocytosis/elliptocytosis syndrome.

Science.gov (United States)

Mentzer, W C; Iarocci, T A; Mohandas, N; Lane, P A; Smith, B; Lazerson, J; Hays, T

1987-01-01

To explain the transient anemia and poikilocytosis seen during infancy in hereditary elliptocytosis (HE), we resealed erythrocyte (RBC) ghosts from affected children or their elliptocytic parents with 2,3-diphosphoglycerate (DPG) (0-8 mM), a compound that dissociates membrane skeletons, then measured ghost mechanical stability in the ektacytometer. Without added 2,3-DPG, ghost mechanical stability was subnormal in infantile poikilocytosis (IP) and HE but was even more abnormal in hereditary pyropoikilocytosis (HPP). Addition of 2,3-DPG (2.55 mM) to IP or HE ghosts, decreased their stability to that of HPP ghosts (without 2,3-DPG). Nonphysiological 2,3-DPG levels (6-8 mM) were required to elicit a similar effect in normal ghosts. The data suggest that free 2,3-DPG, present in neonatal RBC as a consequence of diminished binding to HbF, may render HE susceptible to in vivo fragmentation. The developmental switch from fetal to adult hemoglobin, by diminishing available free 2,3-DPG, may explain the abatement of poikilocytosis and hemolytic anemia that accompanies maturation. Images PMID:3818955

Efficient approach to obtain free energy gradient using QM/MM MD simulation

International Nuclear Information System (INIS)

Asada, Toshio; Koseki, Shiro; Ando, Kanta

2015-01-01

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method

SAXS Study of Sterically Stabilized Lipid Nanocarriers Functionalized by DNA

Science.gov (United States)

Angelov, Borislav; Angelova, Angelina; Filippov, Sergey; Karlsson, Göran; Terrill, Nick; Lesieur, Sylviane; Štěpánek, Petr

2012-03-01

The structure of novel spontaneously self-assembled plasmid DNA/lipid complexes is investigated by means of synchrotron radiation small-angle X-ray scattering (SAXS) and Cryo-TEM imaging. Liquid crystalline (LC) hydrated lipid systems are prepared using the non-ionic lipids monoolein and DOPE-PEG2000 and the cationic amphiphile CTAB. The employed plasmid DNA (pDNA) is encoding for the human protein brain-derived neurotrophic factor (BDNF). A coexistence of nanoparticulate objects with different LC inner organizations is established. A transition from bicontinuous membrane sponges, cubosome intermediates and unilamelar liposomes to multilamellar vesicles, functionalized by pDNA, is favoured upon binding and compaction of pBDNF onto the cationic PEGylated lipid nanocarriers. The obtained sterically stabilized multicompartment nanoobjects, with confined supercoiled plasmid DNA (pBDNF), are important in the context of multicompartment lipid nanocarriers of interest for gene therapy of neurodegenerative diseases.

SAXS Study of Sterically Stabilized Lipid Nanocarriers Functionalized by DNA

International Nuclear Information System (INIS)

Angelov, Borislav; Filippov, Sergey; Štepánek, Petr; Angelova, Angelina; Lesieur, Sylviane; Karlsson, Göran; Terrill, Nick

2012-01-01

The structure of novel spontaneously self-assembled plasmid DNA/lipid complexes is investigated by means of synchrotron radiation small-angle X-ray scattering (SAXS) and Cryo-TEM imaging. Liquid crystalline (LC) hydrated lipid systems are prepared using the non-ionic lipids monoolein and DOPE-PEG 2000 and the cationic amphiphile CTAB. The employed plasmid DNA (pDNA) is encoding for the human protein brain-derived neurotrophic factor (BDNF). A coexistence of nanoparticulate objects with different LC inner organizations is established. A transition from bicontinuous membrane sponges, cubosome intermediates and unilamelar liposomes to multilamellar vesicles, functionalized by pDNA, is favoured upon binding and compaction of pBDNF onto the cationic PEGylated lipid nanocarriers. The obtained sterically stabilized multicompartment nanoobjects, with confined supercoiled plasmid DNA (pBDNF), are important in the context of multicompartment lipid nanocarriers of interest for gene therapy of neurodegenerative diseases.

Scanning slit for HIE-ISOLDE: vibrational test (linear motion actuator from UHV design, speed = 2.5 mm/s)

CERN Document Server

Bravin, E; Sosa, A

2014-01-01

This report summarizes the results of a series of tests performed on the prototype HIE-ISOLDE diagnostic box (HIE-DB) regarding the vibrations and drifts in the transverse position of the scanning blade while moving inside or outside the box. To monitor the transverse position of the blade, a series of 0.1 mm diameter holes were drilled on it and their positions were tracked with an optical system. The linear motion actuator was acquired from UHV design (model LSM38-150-SS), is driven by a stepper motor and has all the guiding mechanisms outside vacuum. The maximum speed of the scanning blade during the tests was 2.5 mm/s. The transverse movement of the slit in the direction perpendicular to the movement was lower than 50 m, and is dominated by the displacement of the contact point of the applied force on the lead-screw. An offset on the slit position was observed while changing the direction of movement of the blade, its amplitude being of the order of 30 m. The amplitudes of the displacements of the transve...

2-cm versus 4-cm surgical excision margins for primary cutaneous melanoma thicker than 2 mm: a randomised, multicentre trial

DEFF Research Database (Denmark)

Gillgren, Peter; Drzewiecki, Krzysztof T; Niin, Marianne

2011-01-01

Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin.......Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin....

Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Yuxin Zhang

2012-02-01

Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.

Climate change under a scenario near 1.5 °C of global warming: monsoon intensification, ocean warming and steric sea level rise

Directory of Open Access Journals (Sweden)

J. Schewe

2011-03-01

Full Text Available We present climatic consequences of the Representative Concentration Pathways (RCPs using the coupled climate model CLIMBER-3α, which contains a statistical-dynamical atmosphere and a three-dimensional ocean model. We compare those with emulations of 19 state-of-the-art atmosphere-ocean general circulation models (AOGCM using MAGICC6. The RCPs are designed as standard scenarios for the forthcoming IPCC Fifth Assessment Report to span the full range of future greenhouse gas (GHG concentrations pathways currently discussed. The lowest of the RCP scenarios, RCP3-PD, is projected in CLIMBER-3α to imply a maximal warming by the middle of the 21st century slightly above 1.5 °C and a slow decline of temperatures thereafter, approaching today's level by 2500. We identify two mechanisms that slow down global cooling after GHG concentrations peak: The known inertia induced by mixing-related oceanic heat uptake; and a change in oceanic convection that enhances ocean heat loss in high latitudes, reducing the surface cooling rate by almost 50%. Steric sea level rise under the RCP3-PD scenario continues for 200 years after the peak in surface air temperatures, stabilizing around 2250 at 30 cm. This contrasts with around 1.3 m of steric sea level rise by 2250, and 2 m by 2500, under the highest scenario, RCP8.5. Maximum oceanic warming at intermediate depth (300–800 m is found to exceed that of the sea surface by the second half of the 21st century under RCP3-PD. This intermediate-depth warming persists for centuries even after surface temperatures have returned to present-day values, with potential consequences for marine ecosystems, oceanic methane hydrates, and ice-shelf stability. Due to an enhanced land-ocean temperature contrast, all scenarios yield an intensification of monsoon rainfall under global warming.

Exploring electronic and steric effects on the insertion and polymerization reactivity of phosphinesulfonato pdii catalysts

KAUST Repository

Neuwald, Boris

2013-11-21

Thirteen different symmetric and asymmetric phosphinesulfonato palladium complexes ([{(X1-Cl)-μ-M}n], M=Na, Li, 1= X(P^O)PdMe) were prepared (see Figure 1). The solid-state structures of the corresponding pyridine or lutidine complexes were determined for (MeO)21-py, (iPrO)21-lut, (MeO,Me2)1-lut, (MeO)31-lut, CF31-lut, and Ph1-lut. The reactivities of the catalysts X1, obtained after chloride abstraction with AgBF4, toward methyl acrylate (MA) were quantified through determination of the rate constants for the first and the consecutive MA insertion and the analysis of β-H and other decomposition products through NMR spectroscopy. Differences in the homo- and copolymerization of ethylene and MA regarding catalyst activity and stability over time, polymer molecular weight, and polar co-monomer incorporation were investigated. DFT calculations were performed on the main insertion steps for both monomers to rationalize the effect of the ligand substitution patterns on the polymerization behaviors of the complexes. Full analysis of the data revealed that: 1) electron-deficient catalysts polymerize with higher activity, but fast deactivation is also observed; 2) the double ortho-substituted catalysts (MeO)21 and (MeO)31 allow very high degrees of MA incorporation at low MA concentrations in the copolymerization; and 3) steric shielding leads to a pronounced increase in polymer molecular weight in the copolymerization. The catalyst properties induced by a given P-aryl (alkyl) moiety were combined effectively in catalysts with two different non-chelating aryl moieties, such as cHexO/(MeO)21, which led to copolymers with significantly increased molecular weights compared to the prototypical MeO1. Catalyst control: The influence of steric and electronic effects on the reactivity of phosphinesulfonato PdII catalysts in polymerization and copolymerization is explored through experimental and DFT methods. A comparison of thirteen different X(P O)PdMe catalysts ((P O)= κ2-P

Design status of the ITER ECRH upper launcher mm-wave system

Energy Technology Data Exchange (ETDEWEB)

Landis, J.-D. [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherches en Physique des Plasmas (CRPP), Association Euratom-Confederation Suisse, 1015 Lausanne (Switzerland)], E-mail: jean-daniel.landis@epfl.ch; Chavan, R.; Bertizzolo, R.; Collazos, A.; Dolizy, F.; Felici, F.; Sanchez, F. [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherches en Physique des Plasmas (CRPP), Association Euratom-Confederation Suisse, 1015 Lausanne (Switzerland); Henderson, M. [ITER, Organization, Cadarache Centre, Saint Paul Lez Durance (France)

2009-06-15

The purpose of the ITER electron cyclotron resonance heating (ECRH) upper launcher (UL), or antennae will be to provide localised current drive by accurately directing mm-wave beams up to 2MW, out of the four allocated upper port plugs, at chosen rational magnetic flux surfaces in order to stabilise neoclassical tearing modes (NTMs). This paper will present an overview of the UL, with emphasis on the mm-wave components. The mm-wave layout includes corrugated waveguide sections and a quasi-optical path with both focusing mirrors and plane steering mirrors. One of the essential components of the UL is the Steering Mechanism Assembly (SMA), providing variable poloidal injection angles fulfilling high deposition accuracy requirements at the plasma location. The Actuator principle and rotor bearings are frictionless and backlash free, avoiding tribological difficulties such as stickslip and seizure. The underlying working principle is the use of mechanically compliant structures. Validation and proof testing of the steering principle is achieved with an uncooled first prototype demonstrator. A second prototype is currently being manufactured, comprising the functionalities needed for the ITER compatible system such as water cooling and high power mm-wave compatibility. In order to perform the fatigue tests of the actuator bellows, a test facility has been built, under ITER-like vacuum and temperature working conditions. Results of the cyclic fatigue tests are compared to the various manufacturer standards and codes, combining stress and strain controlled material fatigue properties.

CT-based postimplant dosimetry of prostate brachytherapy. Comparison of 1-mm and 5-mm section CT

International Nuclear Information System (INIS)

Tanaka, Osamu; Hayashi, Shinya; Kanematsu, Masayuki; Matsuo, Masayuki; Hoshi, Hiroaki; Nakano, Masahiro; Maeda, Sanaho; Deguchi, Takashi; Hoshi, Hiroaki

2007-01-01

The aim of this study was to compare the outcomes between 1-mm and 5-mm section computed tomography (CT)-based postimplant dosimetry. A series of 21 consecutive patients underwent permanent prostate brachytherapy. The postimplant prostate volume was calculated using 1-mm and 5-mm section CT. One radiation oncologist contoured the prostate on CT images to obtain the reconstructed prostate volume (pVol), prostate V 100 (percent of the prostate volume receiving at least the full prescribed dose), and prostate D 90 (mean dose delivered to 90% of the prostate gland). The same radiation oncologist performed the contouring three times to evaluate intraobserver variation and subjectively scored the quality of the CT images. The mean ±1 standard deviation (SD) postimplant pVol was 20.17±6.66 cc by 1-mm section CT and 22.24±8.48 cc by 5-mm section CT; the difference in the mean values was 2.06 cc (P 100 was 80.44%±7.06% by 1-mm section CT and 77.33%±10.22% by 5-mm section CT. The mean postimplant prostate D 90 was 83.28%±10.81% by 1-mm section CT and 78.60%±15.75% by 5-mm section CT. In the evaluation of image quality, 5-mm section CT was assigned significantly higher scores than 1-mm section CT. In regard to intraobserver variation, 5-mm section CT revealed less intraobserver variation than 1-mm section CT. Our current results suggested that the outcomes of postimplant dosimetry using 1-mm section CT did not improved the results over those obtained using 5-mm section CT in terms of the quality of the CT image or reproducibility. (author)

Is 2 mm a safe distance from the inferior alveolar canal to avoid ...

African Journals Online (AJOL)

. Conclusion: When 2 mm is considered as a safety distance, the distance of the implants to the IAC did not yield any statistical difference regarding postoperative neurosensory complications. Keywords: Dental implants, inferior alveolar nerve ...

Survival and photoreactivability of ultraviolet-irradiated cultured fish cells (CAF-MM1)

International Nuclear Information System (INIS)

Mano, Y.; Mitani, H.; Etoh, H.; Egami, N.

1980-01-01

The sensitivity to ultraviolet light (uv) and photoreactivating ability of cultured fish clone cells (CAF-MM1) were investigated. Dose-survival relationship curves were obtained using the colony-forming technique at various postirradiation temperatures (33, 26, and 20 0 C). At 26 0 C the values of D 0 , D/sub q/, and the extrapolation number (n) were 1.74 J/m 2 , 2.62 J/m 2 , and 4.5, respectively; no marked differences in these values were found among different temperatures. Visible light illumination after uv irradiation produced a marked increase in survival. No photoreactivation effects were observed beyond about 30 h. Caffeine increased uv sensitivity of the CAF-MM1 cells, and from the results it is suggested that the cells have some caffeine-sensitive dark repair mechanisms

Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.

Science.gov (United States)

Ibrahim, Mahmoud A A

2011-10-24

The performance of semiempirical molecular-orbital methods--MNDO, MNDO-d, AM1, RM1, PM3 and PM6--in describing halogen bonding was evaluated, and the results were compared with molecular mechanical (MM) and quantum mechanical (QM) data. Three types of performance were assessed: (1) geometrical optimizations and binding energy calculations for 27 halogen-containing molecules complexed with various Lewis bases (Two of the tested methods, AM1 and RM1, gave results that agree with the QM data.); (2) charge distribution calculations for halobenzene molecules, determined by calculating the solvation free energies of the molecules relative to benzene in explicit and implicit generalized Born (GB) solvents (None of the methods gave results that agree with the experimental data.); and (3) appropriateness of the semiempirical methods in the hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme, investigated by studying the molecular inhibition of CK2 protein by eight halobenzimidazole and -benzotriazole derivatives using hybrid QM/MM molecular-dynamics (MD) simulations with the inhibitor described at the QM level by the AM1 method and the rest of the system described at the MM level. The pure MM approach with inclusion of an extra point of positive charge on the halogen atom approach gave better results than the hybrid QM/MM approach involving the AM1 method. Also, in comparison with the pure MM-GBSA (generalized Born surface area) binding energies and experimental data, the calculated QM/MM-GBSA binding energies of the inhibitors were improved by replacing the G(GB,QM/MM) solvation term with the corresponding G(GB,MM) term.

The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II

DEFF Research Database (Denmark)

Elmlund, Hans; Baraznenok, Vera; Lindahl, Martin

2006-01-01

CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Med13, form a repressive module (the Cdk8 module) that prevents RNA polymerase II (pol II) interactions with Mediator. Here, we report that the ability of the Cdk8 module to prevent pol II interactions is independent of the Cdk8......-dependent kinase activity. We use electron microscopy and single-particle reconstruction to demonstrate that the Cdk8 module forms a distinct structural entity that binds to the head and middle region of Mediator, thereby sterically blocking interactions with pol II....

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

Science.gov (United States)

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

Study of the role of bran water binding and the steric hindrance by bran in straight dough bread making.

Science.gov (United States)

Hemdane, S; Langenaeken, N A; Jacobs, P J; Verspreet, J; Delcour, J A; Courtin, C M

2018-07-01

This study investigates the effect of the physical presence and water binding of wheat bran during bread making, and the possible mechanisms behind this effect. Regular bran, pericarp-enriched bran and synthetic bran-like particles with different water binding capacities and particle sizes were used. Incorporation of regular and pericarp-enriched bran in dough (15% dm) led to a lower oven rise than the control dough. Bread volumes decreased with 11% and 30%, respectively. Dough with synthetic bran, having a low water binding capacity, displayed a near to normal leavening and oven rise and resulted in a bread volume decrease of only 5% compared to the control. Particle size reduction of regular bran and synthetic bran to an average size of 200 µm did not affect final bread quality. Results indicate that water binding by bran affects bread quality the most, whereas steric hindrance by physical presence of bran particles is less determinative. Copyright © 2018 Elsevier Ltd. All rights reserved.

R245fa Flow Boiling inside a 4.2 mm ID Microfin Tube

Science.gov (United States)

Longo, G. A.; Mancin, S.; Righetti, G.; Zilio, C.

2017-11-01

This paper presents the R245fa flow boiling heat transfer and pressure drop measurements inside a mini microfin tube with internal diameter at the fin tip of 4.2 mm, having 40 fins, 0.15 mm high with a helix angle of 18°. The tube was brazed inside a copper plate and electrically heated from the bottom. Sixteen T-type thermocouples are located in the copper plate to monitor the wall temperature. The experimental measurements were carried out at constant mean saturation temperature of 30 °C, by varying the refrigerant mass velocity between 100 kg m-2 s-1 and 300 kg m-2 s-1, the vapour quality from 0.15 to 0.95, at two different heat fluxes: 30 and 60 kW m-2. The experimental results are presented in terms of two-phase heat transfer coefficient, onset dryout vapour quality, and frictional pressure drop. Moreover, the experimental measurements are compared against the most updated models for boiling heat transfer coefficient and frictional pressure drop estimations available in the open literature for microfin tubes.

Application of MM wave therapy in radiology

Energy Technology Data Exchange (ETDEWEB)

Avakian, R.S. [Inst. of Radio Physics & Electronics, Ashtarack (Argentina); Gasparyan, L.V. [Republican Medical Centre Armenia, Yerevan (Argentina)

1995-12-31

The authors studied the effects of MM wave electromagnetic radiation influence on patients, affected by X-ray radiation during the reparation works after Chernobyl nuclear power plant exposure. They compared results of treatment of two groups of patients: (1) control group patients received only basis therapy; (2) testing group, 10 patients received basis therapy and MM wave influence. The authors used the wide band noise generator `Artsakh - 2` for local irradiation on the acupuncture points. Their data proved that low intensity MM waves have immunocorrective, antioxidant effects, and MM wave therapy is a perspective method for treatment of patients with radiological pathology.

Clinical comparison between 100 mm photofluorography and digital (1024/sup 2/) fluoroscopic image acquisition

International Nuclear Information System (INIS)

Hynes, D.M.; Edmonds, E.W.; Rowlands, J.A.; Porter, A.J.; Toth, B.D.

1986-01-01

The authors describe current work in progress in which a clinical image can be recorded on both 100-mm film and a 1,024/sup 2/ image store with the same exposure. The 100-mm film is exposed in the usual manner. However, the same radiation exposure is utilized by the optics of the beam splitter to transfer the output image of the intensifier into a 1,024/sup 2/ image store and thence to hard copy by multiformat camera or laser printer. Comparative phantom and clinical images will be presented, along with observations on dose rates needed for diagnostic digital imaging. Use of this system may allow fluoroscopic dose rates to be reduced

Steric and electrostatic interactions govern nanofiltration of amino acids.

Science.gov (United States)

Shim, Yongki; Chellam, Shankararaman

2007-10-01

Crossflow nanofiltration experiments were performed to investigate the factors influencing the removal of amino acids by a commercially available polymeric thin-film composite membrane. The removals of five monoprotic (Ala, Val, Leu, Gly, and Thr), one diprotic (Asp), and one dibasic (Arg) amino acids in a range of permeate fluxes, feed pH values, and ionic strengths were analyzed using a phenomenological model of membrane transport. At any given pH and ionic strength, reflection coefficients (rejection at asymptotically infinite flux) of monoprotic amino acids increased with molar radius demonstrating the role of steric interactions on their removal. Additionally, consistent with Donnan exclusion, higher reflection coefficients were obtained when the membrane and the amino acids both carried the same nature of charge (positive or negative). In other words, both co-ion repulsion and molecular size determined amino acids removal. Importantly, the removal of effectively neutral amino acids were significantly higher than neutral sugars and alcohols of similar size demonstrating that even near their isoelectric point, zwitterionic characteristics preclude them from being considered as strictly neutral. (c) 2007 Wiley Periodicals, Inc.

Performance of ultra-small silicon photomultiplier array with active area of 0.12 mm×0.12 mm

Energy Technology Data Exchange (ETDEWEB)

Yue, Wang; Zongde, Chen; Chenhui, Li; Ran, He; Shenyuan, Wang; Baicheng, Li; Ruiheng, Wang; Kun, Liang, E-mail: lk@bnu.edu.cn; Ru, Yang; Dejun, Han

2015-07-01

We report the performance of an ultra-small silicon photomultiplier (SiPM) line array with 7 elements of 0.12×0.12 mm{sup 2} in active area, 0.2 mm in pitch and 120 micro cells in one element. The device features an epitaxial bulk quenching resistor concept, demonstrated high geometrical fill factor of 41% and photon detection efficiency (PDE) of 25.4% in the wavelength region between 430 nm and 480 nm while retaining high micro cell density around 10 000 mm{sup −2} and ~3 ns FWHM of dark pulses width; it also demonstrated dark count rate of less than 28.7 kHz, optical crosstalk of the order of 2% to 4%, and excellent photon number discrimination. A 0.15 mm×1.6 mm×1.6 mm lutetium yttrium oxyorthosilicate (LYSO) crystal, corresponding to the width, length and height respectively, was successfully coupled to the 1×7 SiPM array for possible ultra-highly resolved positron emission tomography (PET) applications. This novel type of device has advantages particularly for small active area since the performances, such as PDE and response speed is one of the best among SiPMs with similarly high density of micro cells. It may pave a way for this type of SiPM as a promising pixel position sensitive device in imaging sensor applications. - Highlights: • The ultra-small SiPM line array with active area of 0.12 mm×0.12 mm was presented. • The ultra-small SiPM employs the bulk silicon structure as quenching resistor. • A considerable dynamic range and PDE over 25.4% @ 430 nm to 480 nm were characterized.

Results from a partial lifetime test of a 40 mm-aperture 17 mm SSC model dipole

International Nuclear Information System (INIS)

Radusewicz, P.; Devred, A.; Bush, T.; Coombes, R.; DiMarco, J.; Goodzeit, C.; Kuzminski, J.; Ogitsu, T.; Potter, J.; Puglisi, M.; Sanger, P.; Schermer, R.; Tompkins, J.; Yu, Y.; Zhao, Y.; Zheng, H.; Anerella, M.; Cottingham, J.; Ganetis, G.; Garber, M.; Ghosh, A.; Greene, A.; Gupta, R.; Jain, A.; Kahn, S.; Kelly, E.; Morgan, G.; Muratore, J.; Prodell, A.; Rehak, M.; Roher, E.P.; Sampson, W.; Shutt, R.; Thomas, R.; Thompson, P.; Wanderer, P.; Willen, E.; Bleadon, M.; Hanft, R.; Kuchnir, M.; Mantsch, P.; Mazur, P.O.; Orris, D.; Peterson, T.; Strait, J.; Royett, J.; Scanlan, R.; Taylor, C.

1992-03-01

A 40-mm-aperture, 17-m-long Superconducting Super Collider (SSC) model dipole was assembled at Brookhaven National Laboratory (BNL) and tested initially at Fermi National Accelerator Lab (FNAL) and later at BNL. At BNL an extended cycle test was devised to examine the magnet's performance through numerous cold tests and thermal cycles. This paper discusses the magnet's mechanical and quench performance and magnet field measurements during the tests

Sterically screened halogenocyclobutanones. I. Transformations of cyclopropyl-substituted 2,2-dichlorocyclobutanones under the influence of potassium hydroxide

International Nuclear Information System (INIS)

Donskaya, N.A.; Bessmertnykh, A.G.; Drobysh, V.A.; Shabarov, Yu.S.

1987-01-01

The reaction of 2,2-dichloro-3-cyclopropylcyclobutanones with potassium hydroxide was studied. The direction of the reaction depends on the concentration of the potassium hydroxide; with a 2% solution of potassium hydroxide 4,4-dichlorobutyric acids are formed with yields of up to 80%, and with a 15% solution of potassium hydroxide 5-hydroxydihydro-2-furanones are formed with yields of up to 80%. Proposals are made about the mechanism of formation of 5-hydroxydihydro-2-furanones

Recent applications of a QM/MM scheme at the CASPT2//CASSCF/AMBER (or CHARMM) level of theory in photochemistry and photobiology

International Nuclear Information System (INIS)

Sinicropi, A; Basosi, R; Olivucci, M

2008-01-01

The excited-state properties of chemically different chromophores embedded in diverse protein environments or in solution can be nowadays correctly evaluated by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) computational strategy based on multiconfigurational perturbation theory and complete-active-space-self-consistent-field geometry optimization. In particular, in this article we show how a QM/MM strategy has been recently developed in our laboratory and has been successfully applied to the investigation of the fluorescence of the green fluorescent protein (GFP) and how the same strategy (embedding the chromophores in methanol solution) has been combined with retrosynthetic analysis to design a prototype light-driven Z/E molecular switch featuring a single reactive double bond and the same electronic structure and photoisomerization mechanism of the chromophore of the visual pigment Rhodopsin

2-way coupling the hydrological land surface model PROMET with the regional climate model MM5

Directory of Open Access Journals (Sweden)

F. Zabel

2013-05-01

Full Text Available Most land surface hydrological models (LSHMs consider land surface processes (e.g. soil–plant–atmosphere interactions, lateral water flows, snow and ice in a spatially detailed manner. The atmosphere is considered as exogenous driver, neglecting feedbacks between the land surface and the atmosphere. On the other hand, regional climate models (RCMs generally simulate land surface processes through coarse descriptions and spatial scales but include land–atmosphere interactions. What is the impact of the differently applied model physics and spatial resolution of LSHMs on the performance of RCMs? What feedback effects are induced by different land surface models? This study analyses the impact of replacing the land surface module (LSM within an RCM with a high resolution LSHM. A 2-way coupling approach was applied using the LSHM PROMET (1 × 1 km2 and the atmospheric part of the RCM MM5 (45 × 45 km2. The scaling interface SCALMET is used for down- and upscaling the linear and non-linear fluxes between the model scales. The change in the atmospheric response by MM5 using the LSHM is analysed, and its quality is compared to observations of temperature and precipitation for a 4 yr period from 1996 to 1999 for the Upper Danube catchment. By substituting the Noah-LSM with PROMET, simulated non-bias-corrected near-surface air temperature improves for annual, monthly and daily courses when compared to measurements from 277 meteorological weather stations within the Upper Danube catchment. The mean annual bias was improved from −0.85 to −0.13 K. In particular, the improved afternoon heating from May to September is caused by increased sensible heat flux and decreased latent heat flux as well as more incoming solar radiation in the fully coupled PROMET/MM5 in comparison to the NOAH/MM5 simulation. Triggered by the LSM replacement, precipitation overall is reduced; however simulated precipitation amounts are still of high uncertainty, both

Streamer free operation of a 2 mm gap resistive plate chamber with $C_{2}F_{5}H$

CERN Document Server

Cerron-Zeballos, E; Hatzifotiadou, D; Lamas-Valverde, J; Williams, M C S; Zichichi, A

1999-01-01

It is necessary to operate the resistive plate chamber (RPC) in avalanche mode to obtain high efficiency at elevated particle fluxes. We examine this mode of operation with a 2 mm gap RPC using gas mixtures containing C/sub 2/F/sub 4/H/sub 2/ and C/sub 2/F/sub 5/H. In order to explain the data we propose that the avalanche growth is strongly limited by space charge effects. (10 refs).

Influence of steric hindrance on enantioseparation of Dns-amino acids and pesticides on terguride based chiral selectors in capillary electrophoresis

Czech Academy of Sciences Publication Activity Database

Honzátko, Aleš; Cvak, Jan; Vaingátová, Silvie; Flieger, Miroslav

2005-01-01

Roč. 28, - (2005), s. 673-677 ISSN 1615-9306 R&D Projects: GA ČR GA203/02/0933 Institutional research plan: CEZ:AV0Z50200510 Keywords : steric hindrance * capillary electrophoresis * pesticides Subject RIV: EE - Microbiology, Virology Impact factor: 1.829, year: 2005

High speed phototimer and biplane II blanking method in 105 mm RSC photographing of circulatory system

International Nuclear Information System (INIS)

Kaga, Yuji; Kiuchi, Shigeo; Sato, Masami; Komatsuda, Yasushi; Nishio, Kosaku.

1979-01-01

A high speed phototimer as an autoexposure mechanism was developed for 105 mm II indirect continuous photographing of circulatory system. The phototimer can give repeated response of 12 times/sec and the shortest X-ray shut out of 1 m sec. The proper lighting field for the phototimer is 7 mm diameter (12%) of the II input area, equivalent to 80 mm in diameter), and the tube voltage, object property and the focus-II distance characteristics are all well corrected to give good photographs of optimal density. The mutual fog in biplane photographing can be removed by adopting II blanking method. As blanking can respond quite rapidly, photographing time plus 2 m sec is enough for blanking time. That means the positive phase can be brought close to 3 m sec. This mechanism can be applied for biplane cine-photographing. (Kobatake, H.)

On the study of ricochet and penetration in sand, water and gelatin by spheres, 7.62 mm APM2, and 25 mm projectiles

Directory of Open Access Journals (Sweden)

John F. Moxnes

2016-04-01

Full Text Available We examine the ricochet and penetration behavior in sand, water and gelatin by steel spheres, 7.62 mm APM2 and 25 mm projectiles. A threshold impact angle (critical angle exists beyond which ricochet cannot occur. The Autodyn simulation code with the smooth particle hydrodynamic (SPH method and Impetus Afea Solver with the corpuscular model are used and the results are compared with experimental and analytical results. The resistance force in sand for spheres was proportional to a term quadratic in velocity plus a term linear in velocity. The drag coefficient for the quadratic term was 0.65. The Autodyn and Impetus Afea codes simulate too large penetration due to the lack of a linear velocity resistance force. Critical ricochet angles were consistent with analytical results in the literature. In ballistic gelatin at velocities of 50–850 m/s a drag coefficient of 0.30 fits the high speed camera recordings if a linear velocity resistance term is included. However, only a quadratic velocity resistance force with drag coefficient that varies with the Reynolds number also fits the measurements. The simulation of a sphere in water with Autodyn showed too large drag coefficient. The 7.62 mm APM2 core simulations in sand fit reasonable well for both codes. The 25 mm projectile ricochet simulations in sand show consistency with the high speed camera recordings. Computer time was reduced by one to two orders of magnitudes when applying the Impetus Afea Solver compared to Autodyn code due to the use of the graphics processing units (GPU.

Quinoidal Oligo(9,10-anthryl)s with Chain-Length-Dependent Ground States: A Balance between Aromatic Stabilization and Steric Strain Release

KAUST Repository

Lim, Zhenglong; Zheng, Bin; Huang, Kuo-Wei; Liu, Ye; Wu, Jishan

2015-01-01

: the large steric repulsion between the anthryl/phenyl units in the closed-shell quinoidal form that drives the molecule to a flexible open-shell diradical structure, and aromatic stabilisation due to the gain of more aromatic sextet rings in the closed

Initial results from 50mm short SSC dipoles at Fermilab

International Nuclear Information System (INIS)

Bossert, R.C.; Brandt, J.S.; Carson, J.A.; Coulter, K.; Delchamps, S.; Ewald, K.D.; Fulton, H.; Gonczy, I.; Gourlay, S.A.; Jaffery, T.S.; Kinney, W.; Koska, W.; Lamm, M.J.; Strait, J.B.; Wake, M.; Gordon, M.; Hassan, N.; Sims, R.; Winters, M.

1991-03-01

Several short model SSC 50 mm bore dipoles are being built and tested at Fermilab. Mechanical design of these magnets has been determined from experience involved in the construction and testing of 40 mm dipoles. Construction experience includes coil winding, curing and measuring, coil end part design and fabrication, ground insulation, instrumentation, collaring and yoke assembly. Fabrication techniques are explained and construction problems are discussed. Similarities and differences from the 40 mm dipole tooling and management components are outlined. Test results from the first models are presented. 19 refs., 12 figs

Diazo Reagents with Small Steric Footprints for Simultaneous Arming/SAR Studies of Alcohol-Containing Natural Products via O–H Insertion

Science.gov (United States)

Chamni, Supakarn; He, Qing-Li; Dang, Yongjun; Bhat, Shridhar; Liu, Jun O.; Romo, Daniel

2011-01-01

Natural products are essential tools for basic cellular studies leading to the identification of medically relevant protein targets and the discovery of potential therapeutic leads. The development of methods that enable mild and selective derivatization of natural products continues to be of significant interest for mining their information-rich content. Herein, we describe novel diazo reagents for simultaneous arming and structure-activity relationship (SAR) studies of alcohol-containing natural products with a small steric footprint, namely an α-trifluoroethyl (HTFB) substituted reagent. The Rh(II)-catalyzed O–H insertion reaction of several natural products, including the potent translation inhibitor lactimidomycin, was investigated and useful reactivity and both chemo- and site (chemosite) selectivities were observed. Differential binding to the known protein targets of both FK506 and fumagillol was demonstrated, validating the advantage of the smaller steric footprint of trifluoroethyl derivatives. A p-azidophenyl diazo reagent is also described that will prove useful for photoaffinity labeling of low affinity small molecule protein receptors. PMID:21894934

Simple and cheap steric and electronic characterization of the reactivity of Ru(II) complexes containing oxazoline ligands as epoxidation catalysts

KAUST Repository

Poater, Albert

2013-07-01

The reactivity of a new family of complexes with general formula [Ru IV(T)(R-D)(O)]2+ (T = trispyrazolylmethane (tpm); D = N-(1-hydroxy-3-methylbutan-(2S)-(-)-2-yl)-(4S)-(-)-4-isopropyl-4, 5-dihydrooxazole-2-carbimidate, R = Bz (1); iPr (2)) has been analyzed. There is a significant difference in regioselectivity between the two catalysts in the epoxidation of 4-vinylcyclohexene; 1 leads to the regioselective oxidation at the ring alkene position, whereas 2 leads to the oxidation at the terminal position. Although computational calculations indicate small energy differences, both the geometry through steric maps and the electronic parameters of the reactants via conceptual DFT, or charges via NPA, explain the reactivity differences found for the catalysts depending on the substituents of the oxazoline ligands. © 2013 Elsevier B.V. All rights reserved.

A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.

Science.gov (United States)

Kumbhar, Sadhana; Johannsen, Silke; Sigel, Roland K O; Waller, Mark P; Müller, Jens

2013-10-01

A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures. Copyright © 2013 Elsevier Inc. All rights reserved.

Thermoplastic starch composites with TiO2 particles: Preparation, morphology, rheology and mechanical properties.

Science.gov (United States)

Ostafińska, A; Mikešová, J; Krejčíková, S; Nevoralová, M; Šturcová, A; Zhigunov, A; Michálková, D; Šlouf, M

2017-08-01

Composites of thermoplastic starch (TPS) with titanium dioxide particles (mTiO 2 ; average size 0.1μm) with very homogeneous matrix and well-dispersed filler were prepared by a two-step method, including solution casting (SC) followed by melt mixing (MM). Light and scanning electron microscopy confirmed that only the two-step procedure (SC+MM) resulted in ideally homogeneous TPS/mTiO 2 systems. The composites prepared by single-step MM contained non-plasticized starch granules and the composites prepared by single-step SC suffered from mTiO 2 agglomeration. Dynamic mechanical measurements showed an increase modulus with increasing filler concentration. In TPS containing 3wt.% of mTiO 2 the stiffness was enhanced by >40%. Further experiments revealed that the recommended addition of chitosan or the exchange of mTiO 2 for anisometric titanate nanotubes with high aspect ratio did not improve the properties of the composites. Copyright © 2017 Elsevier B.V. All rights reserved.

Steric effects in the dynamics of electrolytes at large applied voltages. II. Modified Poisson-Nernst-Planck equations.

Science.gov (United States)

Kilic, Mustafa Sabri; Bazant, Martin Z; Ajdari, Armand

2007-02-01

In situations involving large potentials or surface charges, the Poisson-Boltzman (PB) equation has shortcomings because it neglects ion-ion interactions and steric effects. This has been widely recognized by the electrochemistry community, leading to the development of various alternative models resulting in different sets "modified PB equations," which have had at least qualitative success in predicting equilibrium ion distributions. On the other hand, the literature is scarce in terms of descriptions of concentration dynamics in these regimes. Here, adapting strategies developed to modify the PB equation, we propose a simple modification of the widely used Poisson-Nernst-Planck (PNP) equations for ionic transport, which at least qualitatively accounts for steric effects. We analyze numerical solutions of these modified PNP equations on the model problem of the charging of a simple electrolyte cell, and compare the outcome to that of the standard PNP equations. Finally, we repeat the asymptotic analysis of Bazant, Thornton, and Ajdari [Phys. Rev. E 70, 021506 (2004)] for this new system of equations to further document the interest and limits of validity of the simpler equivalent electrical circuit models introduced in Part I [Kilic, Bazant, and Ajdari, Phys. Rev. E 75, 021502 (2007)] for such problems.

2nd Conference on Mechanisms, Transmissions and Applications

CERN Document Server

Pinto, Charles; Lovasz, Erwin-Christian

2014-01-01

The Second Conference on Mechanisms, Transmissions and Applications - MeTrApp 2013 was organised by the Mechanical Engineering Department of the University of the Basque Country (Spain) under the patronage of the IFToMM Technical Committees Linkages and Mechanical Controls and Micromachines and the Spanish Association of Mechanical Engineering.  The aim of the workshop was to bring together researchers, scientists, industry experts and students to provide, in a friendly and stimulating environment, the opportunity to exchange know-how and promote collaboration in the field of Mechanism and Machine Science.  The topics treated in this volume are mechanism and machine design, biomechanics, mechanical transmissions, mechatronics, computational and experimental methods, dynamics of mechanisms and micromechanisms and microactuators.

Construction of a positron emission tomograph with 2.4 mm detectors

International Nuclear Information System (INIS)

McIntyre, J.A.; Sprosst, R.L.; Wang, K.

1986-01-01

One-quarter of one ring of a positron tomograph has been constructed. The positron annihilation gamma rays are detected by polished plastic scintillators which direct scintillation light by internal reflection to optical fibers for transmission to the photo-multiplier tubes. By viewing each scintillator with four sets of optical fibers, the number of photomultipliers required for an eight ring tomograph with 1024 detectors per ring (2.4 mm wide detectors) can be reduced from 8192 to 288, and the cost of the tomograph reduced accordingly

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Science.gov (United States)

König, Gerhard; Mei, Ye; Pickard, Frank C; Simmonett, Andrew C; Miller, Benjamin T; Herbert, John M; Woodcock, H Lee; Brooks, Bernard R; Shao, Yihan

2016-01-12

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

Derivation of space groups in mm2, 222 and mmm crystal classes

International Nuclear Information System (INIS)

Nigam, G.D.

1987-08-01

An algebraic approach is developed to derive space groups using 4x4 Seitz matrices for the crystal classes mm2, 222 and mmm in the orthorhombic system. The advantage of the present method is that it is relatively simple and can be adapted to introduce space groups to beginners. One of the advantages of the present method is that it admits a geometrical visualization of the symmetry elements of space group. The method can easily be extended to other crystal classes in a straightforward way. 16 refs, 1 fig., 2 tabs

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

Science.gov (United States)

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

DEFF Research Database (Denmark)

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik

2016-01-01

)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers......The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...

Potential and profile experiments in MM-4

International Nuclear Information System (INIS)

Tian Zhongyu; Ming Linzhou; Feng Xiaozhen; Feng Chuntang; Yin Youjun; Liu Yuhua; Wang Jihai

1988-01-01

Experimental results in MM-4 are presented. These results show that there were double potential wells and double ion temperatures in the plasma. The mechanism giving rise to such potential profiles can be attributed to the Stormer region in the cusp system and the different operation regimes of the electron gun used. The measured plasma potential was about - 200 - 300V

Brownian dynamics simulations of an order-disorder transition in sheared sterically stabilized colloidal suspensions

International Nuclear Information System (INIS)

Rigos, A.A.; Wilemski, G.

1992-01-01

The shear thinning behavior of a sterically stabilized nonaqueous colloidal suspension was investigated using nonequilibrium Brownian dynamics simulations of systems with 108 and 256 particles. At a volume fraction of 0.4, the suspension is thixotropic: it has a reversible shear thinning transition from a disordered state to an ordered, lamellar state with triangularly packed strings of particles. The time scale for the transition is set by the free particle diffusion constant. For the smaller system, the transition occurs gradually with increasing shear rate. For the larger system, the transition is sharp and discontinuous shear thinning is found. 34 refs., 9 figs., 1 tab

A simple and effective solution to the constrained QM/MM simulations

Science.gov (United States)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

A QM/MM study of the reaction mechanism of (R)-hydroxynitrile lyases from Arabidopsis thaliana (AtHNL).

Science.gov (United States)

Zhu, Wenyou; Liu, Yongjun; Zhang, Rui

2015-01-01

Hydroxynitrile lyases (HNLs) catalyze the conversion of chiral cyanohydrins to hydrocyanic acid (HCN) and aldehyde or ketone. Hydroxynitrile lyase from Arabidopsis thaliana (AtHNL) is the first R-selective HNL enzyme containing an α/β-hydrolases fold. In this article, the catalytic mechanism of AtHNL was theoretically studied by using QM/MM approach based on the recently obtained crystal structure in 2012. Two computational models were constructed, and two possible reaction pathways were considered. In Path A, the calculation results indicate that the proton transfer from the hydroxyl group of cyanohydrin occurs firstly, and then the cleavage of C1-C2 bond and the rotation of the generated cyanide ion (CN(-)) follow, afterwards, CN(-) abstracts a proton from His236 via Ser81. The C1-C2 bond cleavage and the protonation of CN(-) correspond to comparable free energy barriers (12.1 vs. 12.2 kcal mol(-1)), suggesting that both of the two processes contribute a lot to rate-limiting. In Path B, the deprotonation of the hydroxyl group of cyanohydrin and the cleavage of C1-C2 bond take place in a concerted manner, which corresponds to the highest free energy barrier of 13.2 kcal mol(-1). The free energy barriers of Path A and B are very similar and basically agree well with the experimental value of HbHNL, a similar enzyme of AtHNL. Therefore, both of the two pathways are possible. In the reaction, the catalytic triad (His236, Ser81, and Asp208) acts as the general acid/base, and the generated CN(-) is stabilized by the hydroxyl group of Ser81 and the main-chain NH-groups of Ala13 and Phe82. © 2014 Wiley Periodicals, Inc.

Re-evaluating the role of sterics and electronic coupling in determining the open-circuit voltage of organic solar cells

KAUST Repository

Graham, Kenneth; Erwin, Patrick; Nordlund, Dennis; Vandewal, Koen; Li, Ruipeng; Ngongang Ndjawa, Guy Olivier; Hoke, Eric T.; Salleo, Alberto; Thompson, Mark E.; McGehee, Michael D.; Amassian, Aram

2013-01-01

The effects of sterics and molecular orientation on the open-circuit voltage and absorbance properties of charge-transfer states are explored in model bilayer organic photovoltaics. It is shown that the open-circuit voltage correlates linearly with the charge-transfer state energy and is not significantly influenced by electronic coupling. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Re-evaluating the role of sterics and electronic coupling in determining the open-circuit voltage of organic solar cells

KAUST Repository

Graham, Kenneth

2013-07-30

The effects of sterics and molecular orientation on the open-circuit voltage and absorbance properties of charge-transfer states are explored in model bilayer organic photovoltaics. It is shown that the open-circuit voltage correlates linearly with the charge-transfer state energy and is not significantly influenced by electronic coupling. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanical characterization and structural of Mg_7_0Zn_2_8Ca_2 alloy for use as bioabsorbable implants

International Nuclear Information System (INIS)

Asato, G.H.; Matias, T.B.; Kiminami, C.S.; Botta, W.J.; Bolfarini, C.

2014-01-01

A ternary magnesium-based alloy was studied for your biocompatibility, high mechanical properties, elastic modulus close to the bone and corrosion rate less than pure magnesium. The experimental conditions enabled to process a Mg70Zn28Ca2 ternary amorphous alloy by the fusion of eutectic binary alloys (Mg-Zn and Mg-Ca), which were obtained from pure elements in a induction furnace in an argon atmosphere. The characterization of alloy involved quantitative chemical analysis, X-ray diffraction (XRD), scanning electron microscopy (SEM) and differential scanning calorimetry (DSC). The results indicated that the actual composition was very close to the nominal, with the presence of amorphous up to 1.3 mm thick. The mechanical compression test was performed in the conventional cylindrical samples with a diameter of 3 mm on an Instron type machine, obtaining the compressive strength above 400 MPa. (author)

Development and application of specially-focused ultrasonic transducers to location and sizing of defects in 75 mm- to 127 mm-thick austenitic stainless steel weld metals

Energy Technology Data Exchange (ETDEWEB)

Dalder, E.N.C.; Benson, S.; McKinley, B.J.; Carodiskey, T.

1992-08-01

Special UT transducer parts, capable of focusing incident signals within a 25 mm {times} 25 mm {times} 25 mm volume in an austenitic stainless weld metal at depths that varied from 25 mm to 127 mm, were developed and demonstrated to be capable of detecting a defect with cross section equivalent to that of a 4.76 mm-dia flat-bottom hole. Defect length sizing could be accomplished to {plus_minus}50% for 100% of the time and to {plus_minus}25% on selected defect types as follows: porosity groups, 100%; cracks, 67%; combined slag and porosity, 60%; and linear slag indications, 59%. Extensive linear elastic-fracture-mechanics analyses were performed to establish allowable defect sizes at functions of stress, based on a cyclic-life criterion of 10{sup 3} full power cycles of the MFTF-B magnet system. These defect sizes were used to determine which UT indicating were to be removed and repaired and which were to be retained and their recorded sizes and locations.

Controlled and Efficient Polymerization of Conjugated Polar Alkenes by Lewis Pairs Based on Sterically Hindered Aryloxide-Substituted Alkylaluminum

Directory of Open Access Journals (Sweden)

Xiaojun Wang

2018-02-01

Full Text Available Reported herein is the development of an effective strategy for controlled and efficient Lewis pair polymerization of conjugated polar alkenes, including methyl methacrylate (MMA, n-butyl methacrylate (nBuMA, and γ-methyl-α-methylene-γ-butyrolactone (γMMBL, by the utilization of sterically encumbered Al(BHT2Me (BHT: 2,6-di-tert-butyl-4-methylphenol as a Lewis acid that shuts down intramolecular backbiting termination. In combination with a selected N-heterocyclic carbene (NHC as a Lewis base, the polymerization of MMA exhibited activity up to 3000 h−1 TOF and an acceptable initiation efficiency of 60.6%, producing polymers with high molecular weight (Mn up to 130 kg/mol and extremely narrow dispersity (Đ = 1.06~1.13. This controlled polymerization with a living characteristic has been evidenced by chain-extension experiments and chain-end analysis, and enabled the synthesis of well-defined diblock copolymers.

CO2-induced mechanical behaviour of Hawkesbury sandstone in the Gosford basin: An experimental study

International Nuclear Information System (INIS)

Rathnaweera, T.D.; Ranjith, P.G.; Perera, M.S.A.; Haque, A.; Lashin, A.; Al Arifi, N.; Chandrasekharam, D; Yang, SQ; Xu, T; Wang, SH; Yasar, E

2015-01-01

Carbon dioxide (CO 2 ) sequestered in saline aquifers undergoes a variety of chemically-coupled mechanical effects, which may cause CO 2 -induced mechanical changes and time-dependent reservoir deformation. This paper investigates the mineralogical and microstructural changes that occur in reservoir rocks following injection of CO 2 in deep saline aquifers and the manner in which these changes influence the mechanical properties of the reservoir rocks. In this study, cylindrical sandstone specimens, 38 mm in diameter and 76 mm high, obtained from the Gosford basin, were used to perform a series of unconfined compressive strength (UCS) tests. Different saturation conditions: dry, water- and brine-saturated sandstone samples with and without scCO 2 (super-critical carbon dioxide) injection, were considered in the study to obtain a comprehensive understanding of the impact of scCO 2 injection during the CO 2 sequestration process on saline aquifer mechanical properties. An acoustic emission (AE) system was employed to identify the stress threshold values of crack closure, crack initiation and crack damage for each testing condition during the whole deformation process of the specimens. Finally, scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray fluorescence (XRF) analyses were performed to evaluate the chemical and mineralogical changes that occur in reservoir rocks during CO 2 injection. From the test results, it is clear that the CO 2 -saturated samples possessed a lower peak strength compared to non-CO 2 saturated samples. According to SEM, XRD and XRF analyses, considerable quartz mineral corrosion and dissolution of calcite and siderite were observed during the interactions of the CO 2 /water/rock and CO 2 /brine/rock systems, which implies that mineralogical and geochemical rock alterations affect rock mechanical properties by accelerating the collapse mechanisms of the pore matrix. AE results also reveal the weakening effect of rock pore

Mechanics of torque generation in the bacterial flagellar motor.

Science.gov (United States)

Mandadapu, Kranthi K; Nirody, Jasmine A; Berry, Richard M; Oster, George

2015-08-11

The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well established that the passage of ions down a transmembrane gradient through the stator complex provides the energy for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify roles for two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, whereas steric forces comprise the actual "power stroke." Specifically, we propose that ion-induced conformational changes about a proline "hinge" residue in a stator α-helix are directly responsible for generating the power stroke. Our model predictions fit well with recent experiments on a single-stator motor. The proposed model provides a mechanical explanation for several fundamental properties of the flagellar motor, including torque-speed and speed-ion motive force relationships, backstepping, variation in step sizes, and the effects of key mutations in the stator.

Quinoidal Oligo(9,10-anthryl)s with Chain-Length-Dependent Ground States: A Balance between Aromatic Stabilization and Steric Strain Release

KAUST Repository

Lim, Zhenglong

2015-11-12

Quinoidal π-conjugated polycyclic hydrocarbons have attracted intensive research interest due to their unique optical/electronic properties and possible magnetic activity, which arises from a thermally excited triplet state. However, there is still lack of fundamental understanding on the factors that determine the electronic ground states. Herein, by using quinoidal oligo(9,10-anthryl)s, it is demonstrated that both aromatic stabilisation and steric strain release play balanced roles in determining the ground states. Oligomers with up to four anthryl units were synthesised and their ground states were investigated by electronic absorption and electron spin resonance (ESR) spectroscopy, assisted by density functional theory (DFT) calculations. The quinoidal 9,10-anthryl dimer 1 has a closed-shell ground state, whereas the tri- (2) and tetramers (3) both have an open-shell diradical ground state with a small singlet-triplet gap. Such a difference results from competition between two driving forces: the large steric repulsion between the anthryl/phenyl units in the closed-shell quinoidal form that drives the molecule to a flexible open-shell diradical structure, and aromatic stabilisation due to the gain of more aromatic sextet rings in the closed-shell form, which drives the molecule towards a contorted quinoidal structure. The ground states of these oligomers thus depend on the overall balance between these two driving forces and show chain-length dependence. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a Prototype 2 mm Fiber-Coupled Seed Laser for Integration in Lidar Transmitter

Data.gov (United States)

National Aeronautics and Space Administration — Optimize the performance of Gallium Antimonide (GaSb)-based 2.05 mm lasers (previously developed under JPL’s Research and Technology Development (R&TD) Program)...

Study of the degradation mechanisms of amines used for the capture of CO2 in industrial fumes

International Nuclear Information System (INIS)

Lepaumier, H.

2008-10-01

Global warming leads to reduce greenhouse gas emissions. Post combustion CO 2 capture with solvent is the most advanced technology to reduce CO 2 emissions in industrial fumes. A major problem associated with chemical absorption of CO 2 using the benchmark ethanolamine (MEA) is solvent degradation through irreversible side reactions with CO 2 and O 2 which leads to numerous harmful impacts to the process: corrosion, solvent loss, foaming, fouling, and viscosity increase. So, developing new amines with higher chemical stability is essential. This work is based on the chemical stability study of 17 different molecules. Their structures have been chosen in order to establish structure-property relationships: alkanolamines, known for gas treatment application (MEA, DEA, MDEA, AMP...), di-amines, and tri-amines without alcohol function. Impact of temperature, CO 2 , and O 2 on degradation has been studied. Strong experimental conditions have been used to observe significant degradation after a 15 days experiment. Separation, identification and quantification of degradation products have been performed by using different testing instructions such as gas chromatography, mass spectrometry, ionic chromatography and NMR. Different mechanisms are proposed to explain most of degradation compounds. Radical reactions (dealkylation, alkylation, ring-closure reactions and piperazinones formation) are involved under O 2 pressure whereas CO 2 induces ionic reactions (dealkylation, alkylation, addition, ring-closure reactions and oxazolidinones or imidazolidinones formation). Large discrepancies of stability are noticed among the different amines. Knowledge of degradation products and reaction mechanisms has thus permitted to establish some relationships between structure and chemical stability: for example, role of the amine function (primary, secondary, tertiary), impact of alkyl chain length between the two amino groups and steric hindrance. (author)

Experimental characteristics of a high-gain free-electron laser amplifier operating at 8-mm and 2-mm wavelengths

International Nuclear Information System (INIS)

Throop, A.L.; Orzechowski, T.J.; Anderson, B.R.

1987-01-01

The Electron Laser Facility (ELF) at the Lawrence Livermore National Laboratory (LLNL) uses a high-current induction linac (3.5 MeV, 1000 A), in conjunction with a pulsed electromagnetic wiggler (4.0 M, 4000 G), to operate a free electron laser (FEL) that produces intense radiation in the microwave regime (2 to 8 mm). ELF is a high-gain, single-pass amplifier, using a commercial microwave source as an oscillator input (200 W-50 kW). Previous experiments at 35 GHz produced exponential gains of 40 dB/m, peak powers exceeding 1 GW, and beam-to-rf conversion efficiencies of 34%. Recent experiments at 140 GHz have demonstrated exponential gains of 22 dB/m, peak powers exceeding 50 MW, and total gains of 65 dB. In this paper, we describe the experimental results at these two frequencies and compare then with the predictions of simulation codes

Analysis of 3D models of octopus estrogen receptor with estradiol: evidence for steric clashes that prevent estrogen binding.

Science.gov (United States)

Baker, Michael E; Chandsawangbhuwana, Charlie

2007-09-28

Relatives of the vertebrate estrogen receptor (ER) are found in Aplysia californica, Octopus vulgaris, Thais clavigera, and Marisa cornuarietis. Unlike vertebrate ERs, invertebrate ERs are constitutively active and do not bind estradiol. To investigate the molecular basis of the absence of estrogen binding, we constructed a 3D model of the putative steroid-binding domain on octopus ER. Our 3D model indicates that binding of estradiol to octopus ER is prevented by steric clashes between estradiol and amino acids in the steroid-binding pocket. In this respect, octopus ER resembles vertebrate estrogen-related receptors (ERR), which have a ligand-binding pocket that cannot accommodate estradiol. Like ERR, octopus ER also may have the activation function 2 domain (AF2) in a configuration that can bind to coactivators in the absence of estrogens, which would explain constitutive activity of octopus ER.

Supersonic Love waves in strong piezoelectrics of symmetry mm2

International Nuclear Information System (INIS)

Darinskii, A. N.; Weihnacht, M.

2001-01-01

A study has been made of the Love wave propagation on piezoelectric substrates of symmetry mm2. It has been shown that under certain conditions the velocity of the Love wave exceeds that of shear horizontal (SH) bulk waves in the substrate. This occurs when the slowness curve of SH bulk waves in the substrate either has a concavity or is convex with nearly zero curvature. For such 'supersonic' Love waves to appear, it is also required that the substrate as well as the layer be specially oriented and that their material constants fulfill a number of inequalities. Numerical computations have been carried out for a number of structures. The results of numerical computations have been compared with approximate analytical estimations. [copyright] 2001 American Institute of Physics

Division of Mechanical Construction - Overview

International Nuclear Information System (INIS)

Halik, J.

2000-01-01

Full text: The Department of Mechanical Construction consists of the Design Group and the Mechanical Workshop. The activity of the Department includes the following:- designs of devices and equipment for experiments in physics and their mechanical construction and assembly, particularly vacuum chambers and installations for HV and UHV; - maintenance and upgrading of the existing installations and equipment in our Institute; - participation of our engineers and technicians in design works, equipment assembly and maintenance for experiments in foreign laboratories. The Design Group is equipped with PC-computers and AutoCad graphic software (release 12 and 13) what allows to make drawings and a mechanical documentation which meets world standards. Also ANSYS (version 5.2) - a software for mechanical, heat and magnetic calculations using finite-elements methods is used in our design activity. The Mechanical Workshop can offer a wide range of machining and treatment methods with satisfactory tolerances and surface quality. The Workshop offers the following possibilities: - turning - cylindrical elements of a length up to 2000 mm and a diameter up to 400 mm, and also disc-type elements of a diameter up to 600 mm and a length not exceeding 300 mm; - milling - elements of length up to 1000 mm and gear wheels of diameter up to 300 mm; - grinding - flat surfaces of dimensions up to 300 mm x 1000 mm and cylindrical elements of a diameter up to 200 mm and a length up to 800 mm; - drilling - holes of a diameter up to 50 mm; - welding - electrical and gas welding, including TIG vacuum-tight welding; - soft and hard soldering; - mechanical works including precision engineering; - plastics treatment - machining and polishing using diamond milling, modelling, lamination of various shapes and materials, including plexiglas, scintillators and light-guides; - painting - paint spraying with possibility of using furnace-fired drier of internal dimensions of 800 mm x 800 mm x 800 mm. Our

Modulation of erythrocyte membrane mechanical stability by 2,3-diphosphoglycerate in the neonatal poikilocytosis/elliptocytosis syndrome.

OpenAIRE

Mentzer, W C; Iarocci, T A; Mohandas, N; Lane, P A; Smith, B; Lazerson, J; Hays, T

1987-01-01

To explain the transient anemia and poikilocytosis seen during infancy in hereditary elliptocytosis (HE), we resealed erythrocyte (RBC) ghosts from affected children or their elliptocytic parents with 2,3-diphosphoglycerate (DPG) (0-8 mM), a compound that dissociates membrane skeletons, then measured ghost mechanical stability in the ektacytometer. Without added 2,3-DPG, ghost mechanical stability was subnormal in infantile poikilocytosis (IP) and HE but was even more abnormal in hereditary p...

Investigation of sheet steel St 37.2 under mechanical impact

International Nuclear Information System (INIS)

Berg, H.P.; Brennecke, P.; Koester, R.; Friehmelt, V.

1990-01-01

Special waste originating, e.g. from chemical industry and radioactive wastes are emplaced in disposal mines. Slinger stowing is an approved technique to fill up residual voids in emplacement rooms. If it should be applied, possible mechanical loads on the integrity of sheet steel containers have to be considered. By theoretical calculations and by experiments under variation of different parameters using test specimen and backfill material from the Konrad mine using the container type V as an example it has been shown that sheet steel St 37.2 with a wall thickness of 3 mm will withstand mechanical impact imposed by backfill particles having a speed of 24 m/s. (orig.) [de

Study of free-radical centers in lignin with 2-mm band ESR spectroscopy

International Nuclear Information System (INIS)

Kuzina, S.I.; Demidov, S.V.; Brezgunov, A.Yu.; Poluehktov, O.G.; Grinberg, O.Ya.; Dubinskij, A.A.; Mikhajlov, A.I.; Lebedev, Ya.S.

1993-01-01

The nature of paramagnetic centers in pristine lignin and lignin, treated with molecular chlorine, aqueous solutions of acids and alkalis, and γ- and UV-irradiated, was studied with 2-mm band ESR spectroscopy. Most of the observed singlet ESR lines are accounted for by radicals with conjugated bonds. High reactivity of double bonds of polyconjugated systems was in the processes studied

Revisiting global mean sea level budget closure : Preliminary results from an integrative study within ESA's Climate Change Initiative -Sea level Budget Closure-Climate Change Initiative

Science.gov (United States)

Palanisamy, H.; Cazenave, A. A.

2017-12-01

The global mean sea level budget is revisited over two time periods: the entire altimetry era, 1993-2015 and the Argo/GRACE era, 2003-2015 using the version '0' of sea level components estimated by the SLBC-CCI teams. The SLBC-CCI is an European Space Agency's project on sea level budget closure using CCI products. Over the entire altimetry era, the sea level budget was performed as the sum of steric and mass components that include contributions from total land water storage, glaciers, ice sheets (Greenland and Antarctica) and total water vapor content. Over the Argo/GRACE era, it was performed as the sum of steric and GRACE based ocean mass. Preliminary budget analysis performed over the altimetry era (1993-2015) results in a trend value of 2.83 mm/yr. On comparison with the observed altimetry-based global mean sea level trend over the same period (3.03 ± 0.5 mm/yr), we obtain a residual of 0.2 mm/yr. In spite of a residual of 0.2 mm/yr, the sea level budget result obtained over the altimetry era is very promising as this has been performed using the version '0' of the sea level components. Furthermore, uncertainties are not yet included in this study as uncertainty estimation for each sea level component is currently underway. Over the Argo/GRACE era (2003-2015), the trend estimated from the sum of steric and GRACE ocean mass amounts to 2.63 mm/yr while that observed by satellite altimetry is 3.37 mm/yr, thereby leaving a residual of 0.7 mm/yr. Here an ensemble GRACE ocean mass data (mean of various available GRACE ocean mass data) was used for the estimation. Using individual GRACE data results in a residual range of 0.5 mm/yr -1.1 mm/yr. Investigations are under way to determine the cause of the vast difference between the observed sea level and the sea level obtained from steric and GRACE ocean mass. One main suspect is the impact of GRACE data gaps on sea level budget analysis due to lack of GRACE data over several months since 2011. The current action plan

Cajaninstilbene acid relaxes rat renal arteries: roles of Ca2+ antagonism and protein kinase C-dependent mechanism.

Directory of Open Access Journals (Sweden)

Dong-Mei Zhang

Full Text Available Cajaninstilbene acid (CSA is a major active component present in the leaves of Cajanus cajan (L. Millsp. The present study explores the underlying cellular mechanisms for CSA-induced relaxation in rat renal arteries. Vascular reactivity was examined in arterial rings that were suspended in a Multi Myograph System and the expression of signaling proteins was assessed by Western blotting method. CSA (0.1-10 µM produced relaxations in rings pre-contracted by phenylephrine, serotonin, 9, 11-dideoxy-9α, 11α-epoxymethanoprostaglandin F(2α (U46619, and 60 mM KCl. CSA-induced relaxations did not show difference between genders and were unaffected by endothelium denudation, nor by treatment with N(G-nitro-L-arginine methyl ester, indomethacin, ICI-182780, tetraethylammonium ion, BaCl(2, glibenclamide, 4-aminopyridine or propranolol. CSA reduced contraction induced by CaCl(2 (0.01-5 mM in Ca(2+-free 60 mM KCl solution and by 30 nM (--Bay K8644 in 15 mM KCl solution. CSA inhibited 60 mM KCl-induced Ca(2+ influx in smooth muscle of renal arteries. In addition, CSA inhibited contraction evoked by phorbol 12-myristate 13-acetate (PMA, protein kinase C agonist in Ca(2+-free Krebs solution. Moreover, CSA reduced the U46619- and PMA-induced phosphorylation of myosin light chain (MLC at Ser19 and myosin phosphatase target subunit 1 (MYPT1 at Thr853 which was associated with vasoconstriction. CSA also lowered the phosphorylation of protein kinase C (PKCδ at Thr505. In summary, the present results suggest that CSA relaxes renal arteries in vitro via multiple cellular mechanisms involving partial inhibition of calcium entry via nifedipine-sensitive calcium channels, protein kinase C and Rho kinase.

2-cm versus 4-cm surgical excision margins for primary cutaneous melanoma thicker than 2 mm: a randomised, multicentre trial

DEFF Research Database (Denmark)

Gillgren, Peter; Drzewiecki, Krzysztof T; Niin, Marianne

2011-01-01

Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin....

Thermo-mechanical design windows for SiC/SiC composite first wall of A-SSTR2

International Nuclear Information System (INIS)

He Kaihui; Satoshi Nishio

2002-01-01

The finite element analysis and calculation is performed for the blanket first wall made of SiC/SiC composite material for Advanced Steady-state Tokamak Reactor 2, A-SSTR2, which is now conceptually designed in Naka Fusion Research Establishment, JAERI. Comparison analysis and design window is analyzed by using the finite element code ADINA 7.4. Through 2D calculation for various geometrical configurations and sensitive material properties, a fundamental guideline for first wall and blanket design is established with respect to maximum temperature, thermal and mechanical stress for many configurations. To satisfy hydrodynamic requirement, a4d4 (the dimension of coolant channel is 4 mm x 8 mm, and the distance between neighboring channels is 4 mm) is chosen as design point for high thermal conductivity up to 50 W/m·K

Observation of spatial resolution of ECR plasma on the MM-2 magnetic mirror

International Nuclear Information System (INIS)

Duan Shuyun; Gu Biao; Guan Weishu; Cheng Shiqing; Liu Rong; Chen Kangwei; Shang Zhenkui

1991-04-01

The measuring method and results of the ECR plasma properties taken from hard X-ray pinhole camera on the MM-2 magnetic mirror are presented. This non-destructive imaging method can directly display the spatial distribution of hot electron plasma. A frame of clear picture could be taken at one shot of discharge. The relationships between emission intensity and discharge parameters are also shown by experimental pictures

Autoregulation of transcription of the hupA gene in Escherichia coli: evidence for steric hindrance of the functional promoter domains induced by HU.

Science.gov (United States)

Kohno, K; Yasuzawa, K; Hirose, M; Kano, Y; Goshima, N; Tanaka, H; Imamoto, F

1994-06-01

The molecular mechanism of autoregulation of expression of the hupA gene in Escherichia coli was examined. The promoter of the gene contains a palindromic sequence with the potential to form a cruciform DNA structure in which the -35 sequence lies at the base of the stem and the -10 sequence forms a single-stranded loop. An artificial promoter lacking the palindrome, which was constructed by replacing a 10 nucleotide repeat for the predicted cruciform arm by a sequence in the opposite orientation, was not subject to HU-repression. DNA relaxation induced by deleting HU proteins and/or inhibiting DNA gyrase in cells results in increased expression from the hupA promoter. We propose that initiation of transcription of the hupA gene is negatively regulated by steric hindrance of the functional promoter domains for formation of the cruciform configuration, which is facilitated at least in part by negative supercoiling of the hupA promoter DNA region. The promoter region of the hupB gene also contains a palindromic sequence that can assume a cruciform configuration. Negative regulation of this gene by HU proteins may occur by a mechanism similar to that operating for the hupA gene.

Coordinated mm/sub-mm observations of Sagittarius A* in May 2007

Energy Technology Data Exchange (ETDEWEB)

Kunneriath, D; Eckart, A; Bertram, T; Konig, S [University of Cologne, Zuelpicher Str. 77, D-50937 Cologne (Germany); Vogel, S [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Sjouwerman, L [National Radio Astronomy Observatory, PO Box 0, Socorro, NM 87801 (United States); Wiesemeyer, H [IRAM, Avenida Divina Pastora, 7, Nuecleo Central, E-18012 Granada (Spain); Schoedel, R [Instituto de AstrofIsica de AndalucIa, Camino Bajo de Huetor 50, 18008 Granada (Spain); Baganoff, F K [Center for Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139-4307 (United States); Morris, M; Mauerhan, J; Meyer, L [Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1547 (United States); Dovciak, M; Karas, V [Astronomical Institute, Academy of Sciences, BocnI II, CZ-14131 Prague (Czech Republic); Dowries, D [Institut de Radio Astronomie Millimetrique, Domaine Universitaire, 38406 St. Martin d' Heres (France); Krichbaum, T; Lu, R-S [Max-Planck-Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Krips, M [Harvard-Smithsonian Center for Astrophysics, SMA project, 60 Garden Street, MS 78 Cambridge, MA 02138 (United States); Markoff, S [Astronomical Institute ' Anton Pannekoek' , University of Amsterdam, Kruislaan 403, 1098SJ Amsterdam (Netherlands); Duschl, W J, E-mail: eckart@phl.uni-koeln.de (and others)

2008-10-15

At the center of the Milky Way, with a distance of {approx}8 kpc, the compact source Sagittarius A* (SgrA*) can be associated with a super massive black hole of {approx}4x 10{sup 6}M{sub o-dot}. SgrA* shows strong variability from the radio to the X-ray wavelength domains. Here we report on simultaneous NIR/sub-millimeter/X-ray observations from May 2007 that involved the NACO adaptive optics (AO) instrument at the European Southern Observatory's Very Large Telescope, the Australian Telescope Compact Array (ATCA), the US mm-array CARMA, the IRAM 30m mm-telescope, and other telescopes. We concentrate on the time series of mm/sub-mm data from CARMA, ATCA, and the MAMBO bolometer at the IRAM 30m telescope.

Diffusion of ionic and non-ionic contrast agents in articular cartilage with increased cross-linking--contribution of steric and electrostatic effects.

Science.gov (United States)

Kulmala, K A M; Karjalainen, H M; Kokkonen, H T; Tiitu, V; Kovanen, V; Lammi, M J; Jurvelin, J S; Korhonen, R K; Töyräs, J

2013-10-01

To investigate the effect of threose-induced collagen cross-linking on diffusion of ionic and non-ionic contrast agents in articular cartilage. Osteochondral plugs (Ø=6mm) were prepared from bovine patellae and divided into two groups according to the contrast agent to be used in contrast enhanced computed tomography (CECT) imaging: (I) anionic ioxaglate and (II) non-ionic iodixanol. The groups I and II contained 7 and 6 sample pairs, respectively. One of the paired samples served as a reference while the other was treated with threose to induce collagen cross-linking. The equilibrium partitioning of the contrast agents was imaged after 24h of immersion. Fixed charge density (FCD), water content, contents of proteoglycans, total collagen, hydroxylysyl pyridinoline (HP), lysyl pyridinoline (LP) and pentosidine (Pent) cross-links were determined as a reference. The equilibrium partitioning of ioxaglate (group I) was significantly (p=0.018) lower (-23.4%) in threose-treated than control samples while the equilibrium partitioning of iodixanol (group II) was unaffected by the threose-treatment. FCD in the middle and deep zones of the cartilage (pionic iodixanol showed no changes in partition after cross-linking, in contrast to anionic ioxaglate, we conclude that the cross-linking induced changes in charge distribution have greater effect on diffusion compared to the cross-linking induced changes in steric hindrance. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

Mechanisms of microbial oil recovery by Clostridium acetobutylicum and Bacillus strain JF-2

Energy Technology Data Exchange (ETDEWEB)

Marsh, T.L.; Zhang, X.; Knapp, R.M.; McInerney, M.J.; Sharma, P.K.; Jackson, B.E.

1995-12-31

Core displacement experiments at elevated pressures were conducted to determine whether microbial processes are effective under conditions that simulate those found in an actual oil reservoir. The in-situ growth of Clostridium acetobutylicum and Bacillus strain JF-2 resulted in the recovery of residual oil. About 21 and 23% of the residual oil was recovered by C. acetobutylicum and Bacillus strain JF-2, respectively. Flooding cores with cell-free culture fluids of C. acetobutylicum with and without the addition of 50 mM acetone and 100 mM butanol did not result in the recovery of residual oil. Mathematical simulations showed that the amount of gas produced by the clostridial fermentation was not showed that the amount of gas produced by the clostridial fermentation was not sufficient to recover residual oil. Oil recovery by Bacillus strain JF-2 was highly correlated to surfactant production. A biosurfactant-deficient mutant of strain JF-2 was not capable of recovering residual oil. These data show that surfactant production is an important mechanism for microbially enhanced oil recovery. The mechanism for oil recovery by C. acetobutylicum is not understood at this time, but the production of acids, solvents, or gases alone cannot explain the observed increases in oil recovery by this organism.

Investigation of CO2 capture mechanisms of liquid-like nanoparticle organic hybrid materials via structural characterization

KAUST Repository

Park, Youngjune

2011-01-01

Nanoparticle organic hybrid materials (NOHMs) have been recently developed that comprise an oligomeric or polymeric canopy tethered to surface-modified nanoparticles via ionic or covalent bonds. It has already been shown that the tunable nature of the grafted polymeric canopy allows for enhanced CO 2 capture capacity and selectivity via the enthalpic intermolecular interactions between CO2 and the task-specific functional groups, such as amines. Interestingly, for the same amount of CO2 loading NOHMs have also exhibited significantly different swelling behavior compared to that of the corresponding polymers, indicating a potential structural effect during CO2 capture. If the frustrated canopy species favor spontaneous ordering due to steric and/or entropic effects, the inorganic cores of NOHMs could be organized into unusual structural arrangements. Likewise, the introduction of small gaseous molecules such as CO2 could reduce the free energy of the frustrated canopy. This entropic effect, the result of unique structural nature, could allow NOHMs to capture CO2 more effectively. In order to isolate the entropic effect, NOHMs were synthesized without the task-specific functional groups. The relationship between their structural conformation and the underlying mechanisms for the CO2 absorption behavior were investigated by employing NMR and ATR FT-IR spectroscopies. The results provide fundamental information needed for evaluating and developing novel liquid-like CO2 capture materials and give useful insights for designing and synthesizing NOHMs for more effective CO2 capture. © the Owner Societies 2011.

Investigation of CO2 capture mechanisms of liquid-like nanoparticle organic hybrid materials via structural characterization.

Science.gov (United States)

Park, Youngjune; Decatur, John; Lin, Kun-Yi Andrew; Park, Ah-Hyung Alissa

2011-10-28

Nanoparticle organic hybrid materials (NOHMs) have been recently developed that comprise an oligomeric or polymeric canopy tethered to surface-modified nanoparticles via ionic or covalent bonds. It has already been shown that the tunable nature of the grafted polymeric canopy allows for enhanced CO(2) capture capacity and selectivity via the enthalpic intermolecular interactions between CO(2) and the task-specific functional groups, such as amines. Interestingly, for the same amount of CO(2) loading NOHMs have also exhibited significantly different swelling behavior compared to that of the corresponding polymers, indicating a potential structural effect during CO(2) capture. If the frustrated canopy species favor spontaneous ordering due to steric and/or entropic effects, the inorganic cores of NOHMs could be organized into unusual structural arrangements. Likewise, the introduction of small gaseous molecules such as CO(2) could reduce the free energy of the frustrated canopy. This entropic effect, the result of unique structural nature, could allow NOHMs to capture CO(2) more effectively. In order to isolate the entropic effect, NOHMs were synthesized without the task-specific functional groups. The relationship between their structural conformation and the underlying mechanisms for the CO(2) absorption behavior were investigated by employing NMR and ATR FT-IR spectroscopies. The results provide fundamental information needed for evaluating and developing novel liquid-like CO(2) capture materials and give useful insights for designing and synthesizing NOHMs for more effective CO(2) capture. This journal is © the Owner Societies 2011

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

QM/MM investigations of organic chemistry oriented questions.

Science.gov (United States)

Schmidt, Thomas C; Paasche, Alexander; Grebner, Christoph; Ansorg, Kay; Becker, Johannes; Lee, Wook; Engels, Bernd

2014-01-01

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar

Buccal mucosa carcinoma: surgical margin less than 3 mm, not 5 mm, predicts locoregional recurrence

Directory of Open Access Journals (Sweden)

Chiou Wen-Yen

2010-09-01

Full Text Available Abstract Background Most treatment failure of buccal mucosal cancer post surgery is locoregional recurrence. We tried to figure out how close the surgical margin being unsafe and needed further adjuvant treatment. Methods Between August 2000 and June 2008, a total of 110 patients with buccal mucosa carcinoma (25 with stage I, 31 with stage II, 11 with stage III, and 43 with Stage IV classified according to the American Joint Committee on Cancer 6th edition were treated with surgery alone (n = 32, surgery plus postoperative radiotherapy (n = 38 or surgery plus adjuvant concurrent chemoradiotherapy (n = 40. Main outcome measures: The primary endpoint was locoregional disease control. Results The median follow-up time at analysis was 25 months (range, 4-104 months. The 3-year locoregional control rates were significantly different when a 3-mm surgical margin (≤3 versus >3 mm, 71% versus 95%, p = 0.04 but not a 5-mm margin (75% versus 92%, p = 0.22 was used as the cut-off level. We also found a quantitative correlation between surgical margin and locoregional failure (hazard ratio, 2.16; 95% confidence interval, 1.14 - 4.11; p = 0.019. Multivariate analysis identified pN classification and surgical margin as independent factors affecting disease-free survival and locoregional control. Conclusions Narrow surgical margin ≤3 mm, but not 5 mm, is associated with high risk for locoregional recurrence of buccal mucosa carcinoma. More aggressive treatment after surgery is suggested.

Buccal mucosa carcinoma: surgical margin less than 3 mm, not 5 mm, predicts locoregional recurrence

International Nuclear Information System (INIS)

Chiou, Wen-Yen; Hung, Shih-Kai; Lin, Hon-Yi; Hsu, Feng-Chun; Lee, Moon-Sing; Ho, Hsu-Chueh; Su, Yu-Chieh; Lee, Ching-Chih; Hsieh, Chen-Hsi; Wang, Yao-Ching

2010-01-01

Most treatment failure of buccal mucosal cancer post surgery is locoregional recurrence. We tried to figure out how close the surgical margin being unsafe and needed further adjuvant treatment. Between August 2000 and June 2008, a total of 110 patients with buccal mucosa carcinoma (25 with stage I, 31 with stage II, 11 with stage III, and 43 with Stage IV classified according to the American Joint Committee on Cancer 6 th edition) were treated with surgery alone (n = 32), surgery plus postoperative radiotherapy (n = 38) or surgery plus adjuvant concurrent chemoradiotherapy (n = 40). Main outcome measures: The primary endpoint was locoregional disease control. The median follow-up time at analysis was 25 months (range, 4-104 months). The 3-year locoregional control rates were significantly different when a 3-mm surgical margin (≤3 versus >3 mm, 71% versus 95%, p = 0.04) but not a 5-mm margin (75% versus 92%, p = 0.22) was used as the cut-off level. We also found a quantitative correlation between surgical margin and locoregional failure (hazard ratio, 2.16; 95% confidence interval, 1.14 - 4.11; p = 0.019). Multivariate analysis identified pN classification and surgical margin as independent factors affecting disease-free survival and locoregional control. Narrow surgical margin ≤3 mm, but not 5 mm, is associated with high risk for locoregional recurrence of buccal mucosa carcinoma. More aggressive treatment after surgery is suggested

The mm-wave compact component of AGN

Science.gov (United States)

Behar, Ehud; Vogel, Stuart; Baldi, Ranieri D.; Smith, Krista L.; Mushotzky, Richard F.

2018-05-01

mm-wave emission from Active Galactic Nuclei (AGN) may hold the key to understanding the physical origin of their radio cores. The correlation between radio/mm and X-ray luminosity may suggest a similar physical origin of the two sources. Since synchrotron self absorption decreases with frequency, mm-waves probe smaller length scales than cm-waves. We report on 100 GHz (3 mm) observations with CARMA of 26 AGNs selected from the hard X-ray Swift/BAT survey. 20/26 targets were detected at 100 GHz down to the 1 mJy (3σ) sensitivity, which corresponds to optically thick synchrotron source sizes of 10-4 - 10-3 pc. Most sources show a 100 GHz flux excess with respect to the spectral slope extrapolated from low frequencies. This mm spectral component likely originates from smaller scales than the few-GHz emission. The measured mm sources lie roughly around the Lmm (100 GHz) ˜10-4LX (2-10 keV) relation, similar to a few previously published X-ray selected sources, and hinting perhaps at a common coronal origin.

The effects of conformational constraints and steric bulk in the amino acid moiety of philanthotoxins on AMPAR antagonism

DEFF Research Database (Denmark)

Jørgensen, Malene; Olsen, Christian A; Mellor, Ian R

2005-01-01

, establishing general protocols for philanthotoxin solution- and solid-phase synthesis (39-90% and 42-54% overall yields, respectively). The analogues were tested for their ability to antagonize kainate-induced currents of 2-amino-3-(3-hydroxy-5-methyl-4-isoxazoyl)propanoic acid receptors (AMPAR) expressed...... in Xenopus oocytes from rat brain mRNA. This showed that steric bulk in the amino acid moiety is well tolerated and suggests that binding to AMPAR does not involve the alpha-NHCO group as a donor in hydrogen bonding.......Philanthotoxin-343 (PhTX-343), a synthetic analogue of wasp toxin PhTX-433, is a noncompetitive antagonist at ionotropic receptors (e.g., AChR or iGluR). To determine possible effects of variations of the amino acid side chain, a library consisting of seventeen PhTX-343 analogues was prepared. Thus...

Rehydrated sterically stabilized phospholipid nanomicelles of budesonide for nebulization: physicochemical characterization and in vitro, in vivo evaluations

Directory of Open Access Journals (Sweden)

Sahib MN

2011-10-01

Full Text Available Mohanad Naji Sahib, Yusrida Darwis, Kok Khiang Peh, Shaymaa Abdalwahed Abdulameer, Yvonne Tze Fung TanSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, MalaysiaBackground: Inhaled corticosteroids provide unique systems for local treatment of asthma or chronic obstructive pulmonary disease. However, the use of poorly soluble drugs for nebulization has been inadequate, and many patients rely on large doses to achieve optimal control of their disease. Theoretically, nanotechnology with a sustained-release formulation may provide a favorable therapeutic index. The aim of this study was to determine the feasibility of using sterically stabilized phospholipid nanomicelles of budesonide for pulmonary delivery via nebulization.Methods: PEG5000-DSPE polymeric micelles containing budesonide (BUD-SSMs were prepared by the coprecipitation and reconstitution method, and the physicochemical and pharmacodynamic characteristics of BUD-SSMs were investigated.Results: The optimal concentration of solubilized budesonide at 5 mM PEG5000-DSPE was 605.71 ± 6.38 µg/mL, with a single-sized peak population determined by photon correlation spectroscopy and a particle size distribution of 21.51 ± 1.5 nm. The zeta potential of BUD-SSMs was -28.43 ± 1.98 mV. The percent entrapment efficiency, percent yield, and percent drug loading of the lyophilized formulations were 100.13% ± 1.09%, 97.98% ± 1.95%, and 2.01% ± 0.02%, respectively. Budesonide was found to be amorphous by differential scanning calorimetry, and had no chemical interaction with PEGylated polymer according to Fourier transform infrared spectroscopy. Transmission electron microscopic images of BUD-SSMs revealed spherical nanoparticles. BUD-SSMs exhibited prolonged dissolution behavior compared with Pulmicort Respules® (P , 0.05. Aerodynamic characteristics indicated significantly higher deposition in the lungs compared with Pulmicort Respules®. The mass median aerodynamic, geometric

Calibration of flavour tagging with B+ -> J/psi(mm)K+ and B0 ->J/psi(mm)K* control channels at LHCb

CERN Document Server

Calvi, M; Leroy, O; Musy, M; Poss, S; Vecchi, S

2009-01-01

B+ -> J/psi(mm)K+ and B0 ->J/psi(mm)K* are suitable control channels for the calibration of flavour tagging for CP measurements in Bs ->J/psi(mm) phi and B0 ->J/psi(mm)KS channels; in the first case if opposite side tagging only is considered. In this note we describe the calibration of the probability of mistag performed with B+ ->J/psi(mm)K+ events and the measurement of the mistag performed with B0 ->J/psi(mm)K* events in a fit to flavour oscillation as a function of proper time. Models are developed to extract this information from selected events taking into account different background components. An expected statistical sensitivity on the average opposite side mistag rate sigma(wOS)/ wOS = 0.3 % is obtained for B0 ->J/psi(mm)K* events, in 2 fb-1 of data.

SSC 40 mm cable results and 50 mm design discussions

International Nuclear Information System (INIS)

Christopherson, D.; Capone, D.; Hannaford, R.; Remsbottom, R.; Delashmit, R.; Jayakumar, R.J.; Snitchler, G.; Scanlan, R.; Royet, J.

1991-01-01

This paper presents a summary of the cable produced for the 1990 40 mm Dipole Program. The cable design parameters for the 50 mm Dipole Program are discussed, as well as portions of the SSC specification draft. Considerations leading to the final cable configuration and the results of preliminary trials are included. The first iteration of a strand mapping program to automate cable strand maps is introduced

A Piezoelectric Micromotor with a Stator of φ=1.6 mm and l=4 mm Using Bulk PZT

Science.gov (United States)

Cagatay, Serra; Koc, Burhanettin; Moses, Paul; Uchino, Kenji

2004-04-01

The smallest discrete piezoelectric ultrasonic motor using bulk ceramics was developed. We are proposing basically a two-part motor: stator and rotor. The stator of the present motor consists of a hollow metal brass tube with outer diameter of 1.6 mm, inner diameter of 0.8 mm and length of only 4 mm with 2 PZT plates bonded onto it. Owing to the asymmetrical stator surface, two degenerated orthogonal bending modes were slightly split, resulting in a wobbling motion. Thus, the motor can be driven by a single driving source. The rotor is a spring, which is basically different from previous designs, pressed at both ends to the stator by a pair of ferrules. Consequently, the length of the whole motor assembly was reduced significantly; a final motor length of only 5 mm was obtained. The working frequency under zero load was approximately 227-233 kHz. Although the size is small, relatively high power was obtained under an optimized load condition: torque of 0.06 mNm, maximum power of 3.2 mW with a speed of 118 rad/s, and maximum efficiency of 11% under 48 Vrms at 221 kHz.

A lithographically patterned capacitor with horizontal nanowires of length 2.5 mm.

Science.gov (United States)

Yan, Wenbo; Thai, Mya Le; Dutta, Rajen; Li, Xiaowei; Xing, Wendong; Penner, Reginald M

2014-04-09

A symmetrical hybrid capacitor consisting of interdigitated, horizontal nanowires is described. Each of the 750 nanowires within the capacitor is 2.5 mm in length, consisting of a gold nanowire core (40 × ≈200 nm) encapsulated within a hemicylindrical shell of δ-phase MnO2 (thickness = 60-220 nm). These Au@δ-MnO2 nanowires are patterned onto a planar glass surface using lithographically patterned nanowire electrodeposition (LPNE). A power density of 165 kW/kg and energy density of 24 Wh/kg were obtained for a typical nanowire array in which the MnO2 shell thickness was 68 ± 8 nm. Capacitors incorporating these ultralong nanowires lost ≈10% of their capacity rapidly, during the first 20 discharge cycles, and then retained 90% of their maximum capacity for the ensuing 6000 cycles. The ability of capacitors consisting of ultralong Au@δ-MnO2 nanowires to simultaneously deliver high power and high capacity with acceptable cycle life is demonstrated.

A comparative study of shadow shield whole body monitor incorporated with 203 mm dia. x 102 mm thick and 102 mm dia. x 76 mm thick NaI(TI) detectors

International Nuclear Information System (INIS)

Sankhla, Rajesh; Singh, I.S.; Rao, D.D.

2016-01-01

The whole body counting using Shadow Shield Whole Body Monitor (SSWBM) proved to be a popular method for assessment of internal contamination due to high energy gamma (E>200 keV) emitting radio nuclides that got inadvertently incorporated in the occupational workers. Currently ∼ 5 SSWBMs are operational at various DAE nuclear facilities throughout the country. The shielding of SSWBMs are said to be designed for 102 mm x 76 mm NaI(Tl) detector and over a period of time, the same concept is being followed. At present, the number of subjects monitored per annum has increased significantly compared to earlier years due to the increase in nuclear facilities at different sites and also increase in number of contract personnel. Aim of this study is to develop/upgrade the existing SSWBMs to increase their capabilities in terms of throughput without compromising on sensitivity. This work includes response studies of individual detectors of sizes 102 mm x 76 mm and 203 mm x 102 mm housed in SSWBM in terms of background, efficiency and Minimum Detection Activity (MDA) for different gamma emitting radio nuclides using Bhabha Atomic Research Centre reference Bottle Mannequin ABsorption (BOMAB) phantom

Bone Ablation at 2.94 mm Using the Free-Electron Laser and Er:YAG Laser

Science.gov (United States)

Ivanov, Borislav; Hakimian, Arman; Peavy, G. M.; Haglund, Richard

2002-03-01

Bone Ablation at 2.94 microns Using the Free-Electron Laser and Er:YAG Laser in Perfluorocarbon Compounds B. Ivanov^1, A. M. Hakimian^1, G. M. Peavy^2, R. F. Haglund, Jr.1 1Department of Physics and Astronomy, W. M. Keck Foundation Free-Electron Laser Center, Vanderbilt University, Nashville, TN 37235 2Beckman Laser Institute and Medical Clinic, College of Medicine, University of California, Irvine, CA 92612 We report studies on the efficiency of mid-IR laser ablation of cow cortical bone using the Vanderbilt free-electron laser (FEL), when irrigating the ablation zone with an inert and biocompatible perfluorocarbon compounds (PFC). At 2.94 microns, the bone matrix (mainly by water) absorbs the radiation while the PFCs transmit this wavelength, dissipate heat and acoustical stress, and prevent carbonization of the bone sample. The ablation rate, as a function of laser fluence, scanning speed and the type of PFC, was investigated. The laser fluence was estimated to be 5 J/cm^2 - 100 J/cm^2 with a laser focal spot diameter of 160 microns 500 microns and a scanning speed of 40 microns/s 2960 microns/s. The ablation rate was estimated from scanning electron microscopy to be 0.5 mm/s 2.4 mm/s. Comparisons of ablation rates with the FEL and a Er:YAG laser at 2.94 microns are being evaluated.

The activation mechanism of Ru-indenylidene complexes in olefin metathesis

KAUST Repository

Urbina-Blanco, Cé sar A.; Poater, Albert; Lé bl, Tomá š; Manzini, Simone; Slawin, Alexandra M. Z.; Cavallo, Luigi; Nolan, Steven P.

2013-01-01

Olefin metathesis is a powerful tool for the formation of carbon-carbon double bonds. Several families of well-defined ruthenium (Ru) catalysts have been developed during the past 20 years; however, the reaction mechanism for all such complexes was assumed to be the same. In the present study, the initiation mechanism of Ru-indenylidene complexes was examined and compared with that of benzylidene counterparts. It was discovered that not all indenylidene complexes followed the same mechanism, highlighting the importance of steric and electronic properties of so-called spectator ligands, and that there is no single mechanism for the Ru-based olefin metathesis reaction. The experimental findings are supported quantitatively by DFT calculations. © 2013 American Chemical Society.

The activation mechanism of Ru-indenylidene complexes in olefin metathesis

KAUST Repository

Urbina-Blanco, César A.

2013-05-08

Olefin metathesis is a powerful tool for the formation of carbon-carbon double bonds. Several families of well-defined ruthenium (Ru) catalysts have been developed during the past 20 years; however, the reaction mechanism for all such complexes was assumed to be the same. In the present study, the initiation mechanism of Ru-indenylidene complexes was examined and compared with that of benzylidene counterparts. It was discovered that not all indenylidene complexes followed the same mechanism, highlighting the importance of steric and electronic properties of so-called spectator ligands, and that there is no single mechanism for the Ru-based olefin metathesis reaction. The experimental findings are supported quantitatively by DFT calculations. © 2013 American Chemical Society.

The "racemic approach" in the evaluation of the enantiomeric NorA efflux pump inhibition activity of 2-phenylquinoline derivatives.

Science.gov (United States)

Carotti, Andrea; Ianni, Federica; Sabatini, Stefano; Di Michele, Alessandro; Sardella, Roccaldo; Kaatz, Glenn W; Lindner, Wolfgang; Cecchetti, Violetta; Natalini, Benedetto

2016-09-10

Among the mechanisms adopted by bacteria, efflux pumps (EPs) have been recognized as being significantly involved in contributing to resistance to commonly used antibacterial agents. However, little is known about their three-dimensional structures or the steric requirements for their inhibition. Lack of such knowledge includes NorA, one of the most studied Staphylococcus aureus EPs. In the present study, the use of two commercialized Cinchona alkaloid-based zwitterionic chiral stationary phases allowed the enantioseparation of four 2-((2-(4-propoxyphenyl)quinolin-4-yl)oxy)alkylamines 1-4 previously found to be potent S. aureus NorA efflux pump inhibitors when tested as racemates. In the identified optimal polar-ionic conditions (MeOH/THF/H2O-49/49/2 (v/v/v)+25mM formic acid, 12.5mM diethylamine), repeated consecutive injections of 1 allowed the isolation of sufficient amount of its enantiomers (2.6mg and 2.8mg, for (R)-1 and (S)-1, respectively) and then to evaluate their ability to inhibit the S. aureus NorA efflux pump. The biological evaluation highlighted the main contribution of the (R)-1 enantiomer to both the EtBr efflux inhibition and synergistic effect with against SA-1199B (norA+/A116E GrlA) respect to the racemate activity. The comparison between the experimental electronic circular dichroism and the time-dependent density functional theory calculations spectra of the two isolated enantiomeric fractions allowed for all compounds a clear and easy assignment of the enantiomeric elution order. Copyright © 2016 Elsevier B.V. All rights reserved.

Fracture Toughness Evaluation of a Ni2MnGa Alloy Through Micro Indentation Under Magneto-Mechanical Loading

Science.gov (United States)

Goanţă, Viorel; Ciocanel, Constantin

2017-12-01

Ni2MnGa is a ferromagnetic alloy that exhibits the shape memory effect either induced by an externally applied magnetic field or mechanical stress. Due to the former, the alloy is commonly called magnetic shape memory alloy or MSMA. The microstructure of the MSMA consists of tetragonal martensite variants (three in the most general case) that are characterized by a magnetization vector which is aligned with the short side of the tetragonal unit cell. Exposing the MSMA to a magnetic field causes the magnetization vector to rotate and align with the external field, eventually leading to variant reorientation. The variant reorientation is observed macroscopically in the form of recoverable strain of up to 6% [1, 2]. As the magnetic field induced reorientation happens instantaneously [1, 3], MSMAs are suitable for fast actuation, sensing, or power harvesting applications. However, actuation applications are limited by the maximum actuation stress of the material that is about 3.5MPa at approximately 2 to 3% reorientation strain. During MSMA fatigue magneto-mechanical characterization studies [4, 5] it was observed that cracks nucleate and grow on the surface of material samples, after a relatively small number of cycles, leading to loss in material performance. This triggered the need for understanding the mechanisms that govern crack nucleation and growth in MSMAs, as well as the nature of the material, i.e. ductile or brittle. The experimental study reported in this paper was carried out to determine material's fracture toughness, the predominant crack growth directions, and the orientation of the cracks relative to the mechanical loading direction and to the material's microstructure. A fixture has been developed to allow Vickers micro indentation of 3mm by 3mm by 20mm Ni2MnGa samples exposed to different levels of magnetic field and/or mechanical stress. Using the measured characteristics of the impression generated during micro indentation, the lengths of

Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study.

Science.gov (United States)

Qi, Yue; Lu, Jiarui; Lai, Wenzhen

2016-05-26

To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.

Microstructure, Mechanical and Corrosion Properties of Friction Stir-Processed AISI D2 Tool Steel

Science.gov (United States)

Yasavol, Noushin; Jafari, Hassan

2015-05-01

In this study, AISI D2 tool steel underwent friction stir processing (FSP). The microstructure, mechanical properties, and corrosion resistance of the FSPed materials were then evaluated. A flat WC-Co tool was used; the rotation rate of the tool varied from 400 to 800 rpm, and the travel speed was maintained constant at 385 mm/s during the process. FSP improved mechanical properties and produced ultrafine-grained surface layers in the tool steel. Mechanical properties improvement is attributed to the homogenous distribution of two types of fine (0.2-0.3 μm) and coarse (1.6 μm) carbides in duplex ferrite-martensite matrix. In addition to the refinement of the carbides, the homogenous dispersion of the particles was found to be more effective in enhancing mechanical properties at 500 rpm tool rotation rate. The improved corrosion resistance was observed and is attributed to the volume fraction of low-angle grain boundaries produced after friction stir process of the AISI D2 steel.

A quantum-mechanics molecular-mechanics scheme for extended systems

International Nuclear Information System (INIS)

Hunt, Diego; Scherlis, Damián A; Sanchez, Veronica M

2016-01-01

We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car–Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (1 0 1) solid–liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces. (paper)

A quantum-mechanics molecular-mechanics scheme for extended systems.

Science.gov (United States)

Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

2016-08-24

We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

Science.gov (United States)

Ojeda-May, Pedro; Pu, Jingzhi

2015-11-07

The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.

Determination and Investigation of Some Physical and Mechanical Properties of Date Fruit (Kabkab Variety

Directory of Open Access Journals (Sweden)

A. M. Kermani

2015-01-01

Full Text Available Knowledge on physical and mechanical properties of fruits is necessary for designing and optimizing processing systems. In this study, several physical and mechanical properties of date fruit (Kabkab cultivar and its seed were determined. The average of length, width, thickness, unit mass, 1000 fruit mass, geometric mean diameter, unit volume, surface and projected areas, sphericity, fruit true and bulk densities, porosity of Kabkab cultivar date fruit were 36.89, 18.68, 23.56 mm, 8264.07 and 8.25 g, 25.24 mm, 8507.8 mm3, 2008.27 mm2, 502.07 mm2, 0.96 g/cm3, 0.51 g/cm3, 46.20%, respectively. The respective values for its seeds were 22.98, 6.25, 7.48 mm, 789.2 and 0.79 g, 10.23 mm, 568.24 mm3, 330.30 mm2, 82.58 mm2, 0.99 g/cm3, 0.65 g/cm3, 30.45%, respectively. The static coefficients of friction were 0.34 for galvanized, 0.30 for steel, 0.32 for plexiglass, 0.31 for glass and 0.42 for plywood. Compressive loading testes were conducted at three loading rates of 5, 15 and 25 mm/min for deformation of fruit until 15%, 30% and 45% of thickness of fruit with seven replications. Some mechanical parameters such as force-deformation, energy and toughness were determined. The results showed that the loading rates affected the mechanical parameters significantly. By increasing the loading rate, the mean values of the mechanical parameters increased significantly.

CO{sub 2}-induced mechanical behaviour of Hawkesbury sandstone in the Gosford basin: An experimental study

Energy Technology Data Exchange (ETDEWEB)

Rathnaweera, T.D. [Department of Civil Engineering, Monash University, Building 60, Melbourne, Victoria 3800 (Australia); Ranjith, P.G., E-mail: ranjith.pg@monash.edu [Department of Civil Engineering, Monash University, Building 60, Melbourne, Victoria 3800 (Australia); Perera, M.S.A.; Haque, A. [Department of Civil Engineering, Monash University, Building 60, Melbourne, Victoria 3800 (Australia); Lashin, A. [King Saud University, College of Engineering-Petroleum and Natural Gas Engineering Department, P.O. Box 800, Riyadh 11421, Saudi Arabia. (Saudi Arabia); Benha University, Faculty of Science-Geology Department, P.O. Box 13518, Benha (Egypt); Al Arifi, N. [King Saud University, College of Science-Geology and Geophysics Department, P.O. Box 2455, Riyadh 11451, Saudi Arabia. (Saudi Arabia); Chandrasekharam, D [King Saud University, College of Science-Geology and Geophysics Department, P.O. Box 2455, Riyadh 11451, Saudi Arabia. (Saudi Arabia); Department of Earth Sciences, Indian Institute of Technology Bombay, 400076 India (India); Yang, SQ [Department of Civil Engineering, Monash University, Building 60, Melbourne, Victoria 3800 (Australia); State Key Laboratory for Geomechanics and Deep Underground Engineering, China University of Mining and Technology, Xuzhou 221116 (China); Xu, T; Wang, SH [Center for Rock Instability & Seismicity Research, Northeastern University, Shenyang 110819 (China); Yasar, E [Iskenderun Technical University, Faculty of Mechanical Engineering, Dept. of Petroleum & Natural Gas Engineering, 31200 (Turkey)

2015-08-12

Carbon dioxide (CO{sub 2}) sequestered in saline aquifers undergoes a variety of chemically-coupled mechanical effects, which may cause CO{sub 2}-induced mechanical changes and time-dependent reservoir deformation. This paper investigates the mineralogical and microstructural changes that occur in reservoir rocks following injection of CO{sub 2} in deep saline aquifers and the manner in which these changes influence the mechanical properties of the reservoir rocks. In this study, cylindrical sandstone specimens, 38 mm in diameter and 76 mm high, obtained from the Gosford basin, were used to perform a series of unconfined compressive strength (UCS) tests. Different saturation conditions: dry, water- and brine-saturated sandstone samples with and without scCO{sub 2} (super-critical carbon dioxide) injection, were considered in the study to obtain a comprehensive understanding of the impact of scCO{sub 2} injection during the CO{sub 2} sequestration process on saline aquifer mechanical properties. An acoustic emission (AE) system was employed to identify the stress threshold values of crack closure, crack initiation and crack damage for each testing condition during the whole deformation process of the specimens. Finally, scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray fluorescence (XRF) analyses were performed to evaluate the chemical and mineralogical changes that occur in reservoir rocks during CO{sub 2} injection. From the test results, it is clear that the CO{sub 2}-saturated samples possessed a lower peak strength compared to non-CO{sub 2} saturated samples. According to SEM, XRD and XRF analyses, considerable quartz mineral corrosion and dissolution of calcite and siderite were observed during the interactions of the CO{sub 2}/water/rock and CO{sub 2}/brine/rock systems, which implies that mineralogical and geochemical rock alterations affect rock mechanical properties by accelerating the collapse mechanisms of the pore matrix. AE results

Film Editing Handbook; Technique of 16mm Film Cutting.

Science.gov (United States)

Churchill, Hugh B.

Designed to help the film student with the complexities of 16mm film cutting, this handbook catalogs the mechanical procedures of both picture and sound cutting and supplies step-by-step explanations of these procedures. Because the handbook was organized so that it could be used while working at the cutting bench, common cutting problems and…

21th CISM-IFToMM Symposium on Theory and Practice of Robots and Manipulators

CERN Document Server

Schiehlen, Werner

2016-01-01

This proceedings volume contains papers that have been selected after review for oral presentation at ROMANSY 2016, the 21th CISM-IFToMM Symposium on Theory and Practice of Robots and Manipulators. These papers cover advances on several aspects of the wide field of Robotics as concerning Theory and Practice of Robots and Manipulators. ROMANSY 2016 is the 21st event in a series that started in 1973 as one of the first conference activities in the world on Robotics. The first event was held at CISM (International Centre for Mechanical Science) in Udine, Italy on 5-8 September 1973. It was also the first topic conference of IFToMM (International Federation for the Promotion of Mechanism and Machine Science) and it was directed not only to the IFToMM community.

Evaluation of cleft lip and palate by computed tomography with 2 mm thin slice scanning, 2

International Nuclear Information System (INIS)

Uchiyama, Mayuki; Tanaka, Hiroshi; Harada, Junta

1992-01-01

Computed tomography was performed on 104 patients with cleft lip and palate by continuous 2 mm slice scanning. The type of hard palate was classified as normal, hypoplasia and aplasia, depending on its developmental degree. The shape of alveolus was also classified as circular, triangular and asymmetric forms for the evaluation of the maxillary development. The hard palate development correlated with the shape of the alveolus, the diameter of maxillary and mandibular bone, and frequency of sinusitis and otitis media. Evaluation of the hard palate by thin slice scanning is useful in presumption of future fecial development. (author)

Evaluation of cleft lip and palate by computed tomography with 2 mm thin slice scanning, 2

Energy Technology Data Exchange (ETDEWEB)

Uchiyama, Mayuki; Tanaka, Hiroshi; Harada, Junta (Jikei Univ., Tokyo (Japan). School of Medicine)

1992-06-01

Computed tomography was performed on 104 patients with cleft lip and palate by continuous 2 mm slice scanning. The type of hard palate was classified as normal, hypoplasia and aplasia, depending on its developmental degree. The shape of alveolus was also classified as circular, triangular and asymmetric forms for the evaluation of the maxillary development. The hard palate development correlated with the shape of the alveolus, the diameter of maxillary and mandibular bone, and frequency of sinusitis and otitis media. Evaluation of the hard palate by thin slice scanning is useful in presumption of future fecial development. (author).

3-D dosimetric evaluation of 2.5 mm HD120 multileaf system for intensity modulated stereotactic radiosurgery using optical CT based polymer gel dosimetry

International Nuclear Information System (INIS)

Wuu, C-S; Kessel, Jack; Xu, Y

2009-01-01

A Trilogy TX equipped with a 2.5 mm HD120 multileaf collimator system is available for the treatment of radiosurgery and IMRT. In this study, we evaluated the 3-D dosimetric impact of leaf width on an IMRT radiosurgery plan by comparing the target coverage and the dose gradient around the target, produced from both a 2.5 mm HD120 high-definition MLC system and a 5mm-leaf-width millennium 120 MLC system, using an optical CT based polymer gel dosimetry system. The 2.5 mm MLC improves target conformity and surrounding tissue sparing when compared to that of 5 mm MLC.

X-ray crystallography and QM/MM investigation on the oligosaccharide synthesis mechanism of rice BGlu1 glycosynthases.

Science.gov (United States)

Wang, Jinhu; Pengthaisong, Salila; Cairns, James R Ketudat; Liu, Yongjun

2013-02-01

Nucleophile mutants of retaining β-glycosidase can act as glycosynthases to efficiently catalyze the synthesis of oligosaccharides. Previous studies proved that rice BGlu1 mutants E386G, E386S and E386A catalyze the oligosaccharide synthesis with different rates. The E386G mutant gave the fastest transglucosylation rate, which was approximately 3- and 19-fold faster than those of E386S and E386A. To account for the differences of their activities, in this paper, the X-ray crystal structures of BGlu1 mutants E386S and E386A were solved and compared with that of E386G mutant. However, they show quite similar active sites, which implies that their activities cannot be elucidated from the crystal structures alone. Therefore, a combined quantum mechanical/molecular mechanical (QM/MM) calculations were further performed. Our calculations reveal that the catalytic reaction follows a single-step mechanism, i.e., the extraction of proton by the acid/base, E176, and the formation of glycosidic bond are concerted. The energy barriers are calculated to be 19.9, 21.5 and 21.9kcal/mol for the mutants of E386G, E386S and E386A, respectively, which is consistent with the order of their experimental relative activities. But based on the calculated activation energies, 1.1kcal/mol energy difference may translate to nearly 100 fold rate difference. Although the rate limiting step in these mutants has not been established, considering the size of the product and the nature of the active site, it is likely that the product release, rather than chemistry, is rate limiting in these oligosaccharides synthesis catalyzed by BGlu1 mutants. Copyright © 2012 Elsevier B.V. All rights reserved.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

Science.gov (United States)

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Extracting dimer structures from simulations of organic-based materials using QM/MM methods

Energy Technology Data Exchange (ETDEWEB)

Pérez-Jiménez, A.J., E-mail: aj.perez@ua.es; Sancho-García, J.C., E-mail: jc.sancho@ua.es

2015-09-28

Highlights: • DFT geometries of isolated dimers in organic crystals differ from experimental ones. • This can be corrected using QM/MM geometry optimizations. • The QM = B3LYP–D3(ZD)/cc-pVDZ and MM = GAFF combination works reasonably well. - Abstract: The functionality of weakly bound organic materials, either in Nanoelectronics or in Materials Science, is known to be strongly affected by their morphology. Theoretical predictions of the underlying structure–property relationships are frequently based on calculations performed on isolated dimers, but the optimized structure of the latter may significantly differ from experimental data even when dispersion-corrected methods are used for it. Here, we address this problem on two organic crystals, namely coronene and 5,6,11,12-tetrachlorotetracene, concluding that it is caused by the absence of the surrounding monomers present in the crystal, and that it can be efficiently cured when the dimer is embedded into a general Quantum Mechanics/Molecular Mechanics (QM/MM) geometry optimization scheme. We also investigate how the size of the MM region affects the results. These findings may be helpful for the simulation of the morphology of active materials in crystalline or glassy samples.

On the IFToMM Permanent Commission for History of MMS

NARCIS (Netherlands)

Ceccarelli, Marco; Koetsier, Teun

2004-01-01

In this paper we have outlined the historical development of the IFToMM Permanent Commission for History of MMS (Mechanism and Machine Science) by also looking at the recently established field of History of MMS with technical perspectives. The activity of the PC for History of MMS has been

Comparison of gas-solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface.

Science.gov (United States)

Rybolt, Thomas R; Bivona, Kevin T; Thomas, Howard E; O'Dell, Casey M

2009-10-01

Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 313-553 K. The molecular adsorbates included: carbon dioxide (CO(2)); tetrafluoromethane (CF(4)); hexafluoroethane (C(2)F(6)); 1,1-difluoroethane (C(2)H(4)F(2)); 1-chloro-1,1-difluoroethane (C(2)H(3)ClF(2)); dichlorodifluoromethane (CCl(2)F(2)); trichlorofluoromethane (CCl(3)F); and 1,1,1-trichloroethane (C(2)H(3)Cl(3)). Two of these molecules are of special interest because they are "super greenhouse gases". The global warming potential, GWP, for CF(4) is 6500 and for C(2)F(6) is 9200 relative to the reference value of 1 for CO(2). The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule-surface binding energy, could avoid atmospheric release. The temperature variations of the gas-solid virial coefficients in conjunction with van't Hoff plots were used to find the experimental adsorption energy or binding energy values (E(*)) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (Ecal(*)) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule-surface interactions for Carbopack B. Linear regressions of E(*) versus Ecal(*) for the current data set of eight molecules and the same surface model gave E(*)=0.926 Ecal(*) and r(2)=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes

Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.

Science.gov (United States)

Plotnikov, Nikolay V; Prasad, B Ram; Chakrabarty, Suman; Chu, Zhen T; Warshel, Arieh

2013-10-24

Understanding the nature of the free-energy surfaces for phosphate hydrolysis is a prerequisite for understanding the corresponding key chemical reactions in biology. Here, the challenge has been to move to careful ab initio QM/MM (QM(ai)/MM) free-energy calculations, where obtaining converging results is very demanding and computationally expensive. This work describes such calculations, focusing on the free-energy surface for the hydrolysis of phosphate monoesters, paying special attention to the comparison between the one water (1W) and two water (2W) paths for the proton-transfer (PT) step. This issue has been explored before by energy minimization with implicit solvent models and by nonsystematic QM/MM energy minimization, as well as by nonsystematic free-energy mapping. However, no study has provided the needed reliable 2D (3D) surfaces that are necessary for reaching concrete conclusions. Here we report a systematic evaluation of the 2D (3D) free-energy maps for several relevant systems, comparing the results of QM(ai)/MM and QM(ai)/implicit solvent surfaces, and provide an advanced description of the relevant energetics. It is found that the 1W path for the hydrolysis of the methyl diphosphate (MDP) trianion is 6-9 kcal/mol higher than that the 2W path. This difference becomes slightly larger in the presence of the Mg(2+) ion because this ion reduces the pKa of the conjugated acid form of the phosphate oxygen that accepts the proton. Interestingly, the BLYP approach (which has been used extensively in some studies) gives a much smaller difference between the 1W and 2W activation barriers. At any rate, it is worth pointing out that the 2W transition state for the PT is not much higher that the common plateau that serves as the starting point of both the 1W and 2W PT paths. Thus, the calculated catalytic effects of proteins based on the 2W PT mechanistic model are not expected to be different from the catalytic effects predicted using the 1W PT mechanistic

X-ray analytics for 450-mm wafer; Roentgenanalytik fuer 450-mm-Wafer

Energy Technology Data Exchange (ETDEWEB)

Anon.

2014-09-15

The introduction of the 450-mm technology in the wafer fabrication and the further reduction of critical dimensions requires improved X-ray analysis methods. Therefor the PTB has concipated a metrology chamber for the characterization of 450-mm wafers, the crucial element of which is a multi-axis patent-pending manipulator.

ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

Science.gov (United States)

Stolworthy, L D; Shirts, R B

1997-03-01

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

Simulation with quantum mechanics/molecular mechanics for drug discovery.

Science.gov (United States)

Barbault, Florent; Maurel, François

2015-10-01

Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

Investigation of the physical and mechanical properties of Shea Tree ...

African Journals Online (AJOL)

Investigation of the physical and mechanical properties of Shea Tree timber ( Vitellaria paradoxa ) used for structural applications in Kwara State, Nigeria. ... strength parallel to grain of 24.7 (N/mm2), compressive strength perpendicular to grain of 8.99 (N/mm2), shear strength of 2.01 (N/mm2), and tensile strength parallel to ...

Steric exclusion and protein conformation determine the localization of plasma membrane transporters.

Science.gov (United States)

Bianchi, Frans; Syga, Łukasz; Moiset, Gemma; Spakman, Dian; Schavemaker, Paul E; Punter, Christiaan M; Seinen, Anne-Bart; van Oijen, Antoine M; Robinson, Andrew; Poolman, Bert

2018-02-05

The plasma membrane (PM) of Saccharomyces cerevisiae contains membrane compartments, MCC/eisosomes and MCPs, named after the protein residents Can1 and Pma1, respectively. Using high-resolution fluorescence microscopy techniques we show that Can1 and the homologous transporter Lyp1 are able to diffuse into the MCC/eisosomes, where a limited number of proteins are conditionally trapped at the (outer) edge of the compartment. Upon addition of substrate, the immobilized proteins diffuse away from the MCC/eisosomes, presumably after taking a different conformation in the substrate-bound state. Our data indicate that the mobile fraction of all integral plasma membrane proteins tested shows extremely slow Brownian diffusion through most of the PM. We also show that proteins with large cytoplasmic domains, such as Pma1 and synthetic chimera of Can1 and Lyp1, are excluded from the MCC/eisosomes. We hypothesize that the distinct localization patterns found for these integral membrane proteins in S. cerevisiae arises from a combination of slow lateral diffusion, steric exclusion, and conditional trapping in membrane compartments.

QM/MM Molecular Dynamics Studies of Metal Binding Proteins

Directory of Open Access Journals (Sweden)

Pietro Vidossich

2014-07-01

Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface

Energy Technology Data Exchange (ETDEWEB)

Yang Zhenyu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080(China); Zhao Yapu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: yzhao@lnm.imech.ac.cn

2006-05-15

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by 'GAMESS', and the rest atoms are treated as MM part calculated by 'TINKER'. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Steric control of the donor/acceptor interface: Implications in organic photovoltaic charge generation

KAUST Repository

Holcombe, Thomas W.; Norton, Joseph E.; Rivnay, Jonathan; Woo, Claire; Goris, Ludwig J.; Piliego, Claudia; Griffini, Gianmarco; Sellinger, Alan; Bré das, Jean Luc; Salleo, Alberto; Frechet, Jean

2011-01-01

The performance of organic photovoltaic (OPV) devices is currently limited by modest short-circuit current densities. Approaches toward improving this output parameter may provide new avenues to advance OPV technologies and the basic science of charge transfer in organic semiconductors. This work highlights how steric control of the charge separation interface can be effectively tuned in OPV devices. By introducing an octylphenyl substituent onto the investigated polymer backbones, the thermally relaxed charge-transfer state, and potentially excited charge-transfer states, can be raised in energy. This decreases the barrier to charge separation and results in increased photocurrent generation. This finding is of particular significance for nonfullerene OPVs, which have many potential advantages such as tunable energy levels and spectral breadth, but are prone to poor exciton separation efficiencies. Computational, spectroscopic, and synthetic methods were combined to develop a structure-property relationship that correlates polymer substituents with charge-transfer state energies and, ultimately, device efficiencies. © 2011 American Chemical Society.

Steric control of the donor/acceptor interface: Implications in organic photovoltaic charge generation

KAUST Repository

Holcombe, Thomas W.

2011-08-10

The performance of organic photovoltaic (OPV) devices is currently limited by modest short-circuit current densities. Approaches toward improving this output parameter may provide new avenues to advance OPV technologies and the basic science of charge transfer in organic semiconductors. This work highlights how steric control of the charge separation interface can be effectively tuned in OPV devices. By introducing an octylphenyl substituent onto the investigated polymer backbones, the thermally relaxed charge-transfer state, and potentially excited charge-transfer states, can be raised in energy. This decreases the barrier to charge separation and results in increased photocurrent generation. This finding is of particular significance for nonfullerene OPVs, which have many potential advantages such as tunable energy levels and spectral breadth, but are prone to poor exciton separation efficiencies. Computational, spectroscopic, and synthetic methods were combined to develop a structure-property relationship that correlates polymer substituents with charge-transfer state energies and, ultimately, device efficiencies. © 2011 American Chemical Society.

A structural study of [CpM(CO)3H] (M = Cr, Mo and W) by single-crystal X-ray diffraction and DFT calculations: sterically crowded yet surprisingly flexible molecules.

Science.gov (United States)

Burchell, Richard P L; Sirsch, Peter; Decken, Andreas; McGrady, G Sean

2009-08-14

The single-crystal X-ray structures of the complexes [CpCr(CO)3H] 1, [CpMo(CO)3H] 2 and [CpW(CO)3H] 3 are reported. The results indicate that 1 adopts a structure close to a distorted three-legged piano stool geometry, whereas a conventional four-legged piano stool arrangement is observed for 2 and 3. Further insight into the equilibrium geometries and potential energy surfaces of all three complexes was obtained by DFT calculations. These show that in the gas phase complex 1 also prefers a geometry close to a four-legged piano stool in line with its heavier congeners, and implying strong packing forces at work for 1 in the solid state. Comparison with their isolelectronic group 7 tricarbonyl counterparts [CpM(CO)3] (M = Mn 4 and Re 5) illustrates that 1, 2 and 3 are sterically crowded complexes. However, a surprisingly soft bending potential is evident for the M-H moiety, whose order (1 approximately = 2 < 3) correlates with the M-H bond strength rather than with the degree of congestion at the metal centre, indicating electronic rather than steric control of the potential. The calculations also reveal cooperative motions of the hydride and carbonyl ligands in the M(CO)3H unit, which allow the M-H moiety to move freely, in spite of the closeness of the four basal ligands, helping to explain the surprising flexibility of the crowded coordination sphere observed for this family of high CN complexes.

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

Science.gov (United States)

Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

2018-03-01

The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

Transportation studies: 40-MM collider dipole magnets

International Nuclear Information System (INIS)

Daly, E.

1992-01-01

Several fully functional 40-mm Collider Dipole Magnets (CDM) were instrumented with accelerometers to monitor shock and vibration loads during transport. The magnets were measured with optical tooling telescopes before and after transport. Changes in mechanical alignment due to shipping and handling were determined. The mechanical stability of the cryogen lines were checked using the same method. Field quality and dipole angle were measured warm before and after transport to determine changes in these parameters. Power spectra were calculated for accelerometers located on the cold mass, vacuum vessel, and trailer bed. Where available, plots of field quality and dipole roll both before and after were created. Shipping loads measured were largest in the vertical direction, where most of the structural deformation of the magnet was evident. It was not clear that magnetic performance was affected by the shipping and handling environment

Critical heat flux of R134A and R245FA in a 2.2 mm circular tube

Energy Technology Data Exchange (ETDEWEB)

Tibirica, Cristiano Bigonha; Ribatski, Gherhardt [Universidade de Sao Paulo (EESC/USP), Sao Carlos, SP (Brazil). Escola de Engenharia. Dept. de Engenharia Mecanica], E-mails: bigonha@sc.usp.br, ribatski@sc.usp.br; Szczukiewicz, Sylwia; Thome, John Richard [Ecole Polytechnique Federale de Lausanne (LTCM/EPFL) (Switzerland). Lab. of Heat and Mass Transfer], Emails: sylwia.szczukiewicz@epfl.ch, john.thome@epfl.ch

2010-07-01

Critical heat flux (CHF) during flow boiling is generally related to a drastic decrease in the heat transfer coefficient and it is the maximum operational heat flux that can be achieved under safe operation. Due to such a fact, this topic has attracted great attention of the academic society dealing with boiling heat transfer and also in the industrial sector involved with the dissipation of high heat flux densities. In the specific case of high heat flux densities, micro-channel flow boiling is a promising technique for pursuing this objective. The boundary where microscale effects start in flow boiling is still an open issue in the literature and a 3 mm internal diameter (ID) threshold value, as suggested by Kandlikar and Grande (2003) is frequently adopted to characterize this point. Considering the needs for a better understanding of the micro/macro transition, this paper presents new experimental critical heat flux results in saturated flow boiling conditions for a macro/micro-scale tube. The data were obtained in a horizontal 2.20 mm ID stainless steel tube with heating lengths of 361 and 154 mm, R134a and R245fa as working fluids, mass velocities ranging from 100 to 1500 kg/m{sup 2s}, critical heat fluxes from 25 to 300 kW/m2, exit saturation temperatures of 25, 31 and 35 degree C, and critical vapor qualities ranging from 0.55 to 1. The experimental results show that critical heat flux increases with increasing mass velocity and inlet subcooling but decreases with increasing saturation temperature and heated length. The data also indicated a higher CHF for R245fa when compared with R134a at similar conditions. The experimental data were compared against the following CHF predictive methods: Katto and Ohno (1984), Shah (1987), Zhang et al. (2006) and Ong and Thome(2010). Katto and Ohno (1984) and Ong and Thome (2010) best predicted the database with a mean average error smaller than 15%. Both correlations include low and high pressure fluids in their

Enhancement of Mechanical Properties of Extruded Mg-9Al-1Zn-1MM-0.7CaO-0.3Mn Alloy Through Pre-aging Treatment

Science.gov (United States)

Jeong, Seok Hoan; Kim, Yong Joo; Kong, Kyung Ho; Cho, Tae Hee; Kim, Young Kyun; Lim, Hyun Kyu; Kim, Won Tae; Kim, Do Hyang

2018-03-01

The effect of pre-aging treatment before extrusion has been investigated in Mg-9.0Al-1.0Zn-1MM-0.7CaO-0.3Mn alloy. The as-cast microstructure consists of α-Mg dendrite with secondary solidification phase particles, (Mg, Al)2Ca, β-Mg17Al12 and Al11RE3 at the inter-dendritic region. After extrusion, β-Mg17Al12 precipitates are present, but higher density and more homogeneous distribution in pre-aged alloy. In addition, μm-scale banded bulk β-Mg17Al12 particles are generated during extrusion. Al11RE3 particles are broken into small particles, and are aligned along the extrusion direction. (Mg, Al)2Ca particles are only slightly elongated along the extrusion direction, providing stronger particle stimulated nucleation (PSN) effect by severe deformation during extrusion. The mechanical properties can be significantly enhanced by introducing pre-aging treatment, i.e. β-Mg17Al12 precipitates provide grain refining and strengthening effects and (Mg, Al)2Ca particles provide PSN effect.

Experimentally stabilized superconducting magnet with inner diameter of 700 mm

Energy Technology Data Exchange (ETDEWEB)

Vetlitskii, I A; Belonogov, A V; Dobrov, V M; Krylov, V L; Lebedev, A V; Lomkatsi, G S; Nilov, A F; Smolyankin, V T

1974-05-01

An experimental magnet, SPM-70, with the following characteristics was constructed. The inner diameter of the winding was 730 mm; outer diameter of the winding 1000 mm; height of winding 310 mm; magnetic induction at the center of the magnet 1.45 T; maximum magnetic induction 2.4 T; operation current 820 A; ampere-turns 1.07 x 10/sup 6/; design current density 2560 A/cm/sup 2/; stored energy 500 kJ; superconducting alloy Nb+50% Zr; weight of superconductor 23 kg; weight of copper 210 kg; resistivity of the copper in the strips at T = 4.2 K, B = 2.5 T, 2.6 x 10/sup -8/ ..cap omega.. cm.

Chapter 1. General information about uranium. 1.5. Mechanical properties

International Nuclear Information System (INIS)

Khakimov, N.; Nazarov, Kh.M.; Mirsaidov, I.U.

2012-01-01

Full text: The mechanical properties of uranium depend on its purity, and which mechanical and thermal regimes are used for reprocessing. The average elasticity module value for cast uranium is 20.5•10"-"2 mega newton/m"2 (20.9•10"-"3 kilogram-force/mm"2), strength limit during tension at room temperature is 372–470 mega newton/m"2 (38–48 kilogram-force/mm"2), strength is increased after hardening from β - and γ - phases; and average rigidity by Brinell 19.6–21.6•10"2 mega newton/m"2 (200–220 kilogram-force/mm"2). Exposure by neutron flux (which occurs in nuclear reactors) changes the physical and mechanical properties of uranium: creeping develops and brittleness increases, goods deformation is observed, which forces the operator to use uranium in nuclear reactors as different uranium alloys.

Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.

Science.gov (United States)

Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu

2013-09-10

Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying

How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

Directory of Open Access Journals (Sweden)

Yanwei Li

2016-08-01

Full Text Available The quantum mechanics/molecular mechanics (QM/MM method (e.g., density functional theory (DFT/MM is important in elucidating enzymatic mechanisms. It is indispensable to study “multiple” conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.

HTS Nested magnet wound with 12 mm GdBCO tape and 4.4 mm YBCO tape

International Nuclear Information System (INIS)

Kang, Myung Hun; Ku, Myung Hwan; Cha, Guee Soo; Lim, Hyoung Woo

2015-01-01

The properties of High Temperature Superconducting (HTS) tapes are progressing, as HTS tapes evolve from 1st generation to 2nd generation. This paper presents design and construction of a 2nd generation HTS magnet consisting of two nested GdBCO and YBCO pancake coils. Two HTS tapes of different widths were used to wind the HTS nested magnet. Considering that a higher magnetic field is applied to the inner magnet than to the outer magnet, 12 mm GdBCO tape was used for winding the inner magnet, which consisted of four single pancake windings. Eight double pancake windings wound with 4.4 mm YBCO tapes were used for the outer magnet. The test results show that the central magnetic field of the HTS nested magnet was 920 mT. The measured critical currents of the inner and outer magnet at 77K were 80.8 A and 32.6 A, respectively

Effects of gripping volume in the mechanical strengths of orthodontic mini-implant

Directory of Open Access Journals (Sweden)

Yu-Chuan Tseng

2017-11-01

Full Text Available The objective of study was to investigate the correlation between the mechanical strengths [insertion torque (IT; resonance frequency (RF; and horizontal pullout strength (HPS] and gripping volume (GV of mini-implants. Thirty mini-implants of three types (Type A: 2 mm × 10 mm, cylindrical, titanium alloy; Type B: 2 mm × 10 mm, tapered, stainless steel; and Type C: 2 mm × 11 mm, cylindrical, titanium alloy were inserted 7 mm into artificial bones. One-way analysis of variance and Spearman's test were applied to assess intergroup comparisons and intragroup correlations. The null hypothesis was that no statistically significant correlations exist between the GV and mechanical strengths (IT, RF, and HPS. In the IT test, Type C (14.2 Ncm had significantly (p=0.016 greater values than did Type A (12.4 Ncm. In the RF analysis, no significant difference was observed among the three types of mini-implants. In the HPS test, Type C (388.9 Ncm was significantly larger than both Type B (294.5 Ncm and Type A (286 Ncm. In the GV measurement, Type C (14.4 mm3 was significantly larger than Type B (11.4 mm3 and Type A (9.2 mm3. Type A and Type B exhibited no significant correlations among the tests. Therefore, the null hypothesis was accepted. Although no significant correlation was noted between the GV and mechanical strengths (IT, RF, and HPS, we observed a trend that the mechanical strengths (IT, RF, and HPS of the mini-implants corresponded to the order and values of GV (Type C > Type B > Type A.

Nimbus-2 High-Resolution Infrared Radiometer (HRIR) Imagery of Cloud Cover at Night on 70 mm Film V001

Data.gov (United States)

National Aeronautics and Space Administration — The HRIRN2IM data product contains scanned negatives of photofacsimile 70mm film strips from the Nimbus-2 High-Resolution Infrared Radiometer. The images contain...

Análise do uso da membrana cerâmica de 0,2 μm na clarificação de cerveja = Analysis of the use of a 0.2 mm ceramic membrane for beer clarification

Directory of Open Access Journals (Sweden)

Tatiana Valesca Rodríguez Alicieo

2008-07-01

Full Text Available Neste trabalho são comparados o fluxo permeado e a qualidade do produto obtido na clarificação de cerveja por microfiltração tangencial, para uma membrana cerâmica tubular com tamanho nominal de poro de 0,2 mm na temperatura de 6 ± 1°C e pressões de 1, 2, 3 e 4 bar. Amostras do alimentado e permeado foram submetidas a análisesfísico-químicas. Além disso, foi realizado o estudo do mecanismo de fouling: bloqueio completo, bloqueio parcial e bloqueio interno de poros e formação de torta. Os resultados mostram redução de cor de 28,75% e de turbidez de 95,65% para a pressão de 4 bar. O estudo de fouling demonstrou que o mecanismo para a pressão de 1 e 3 bar foi o de bloqueio completo de poros e para a pressão de 2 e 4 bar o de formação de torta.This work compares the permeated flow and the quality of the obtainedproduct in the process of beer clarification by crossflow microfiltration. The membrane used in the present study was a tubular ceramic membrane with a 0.2 mm nominal pore diameter, at 6 ± 1°C and 1, 2, 3 and 4 bar of pressure. Samples of the feed and permeatewere analyzed. Additionally, the fouling mechanism was studied: complete, partial, internal blockade of pores and cake filtration. The results show a 28.75% reduction in color and 95.65% in turbidity at 4 bar. The study of fouling showed that the mechanism used for thepressures of 1 and 3 bar was the complete blockade of pores, whereas for the pressures of 2 and 4 bar, the cake formation was the mechanism used.

Emergence of two prion subtypes in ovine PrP transgenic mice infected with human MM2-cortical Creutzfeldt-Jakob disease prions.

Science.gov (United States)

Chapuis, Jérôme; Moudjou, Mohammed; Reine, Fabienne; Herzog, Laetitia; Jaumain, Emilie; Chapuis, Céline; Quadrio, Isabelle; Boulliat, Jacques; Perret-Liaudet, Armand; Dron, Michel; Laude, Hubert; Rezaei, Human; Béringue, Vincent

2016-02-05

Mammalian prions are proteinaceous pathogens responsible for a broad range of fatal neurodegenerative diseases in humans and animals. These diseases can occur spontaneously, such as Creutzfeldt-Jakob disease (CJD) in humans, or be acquired or inherited. Prions are primarily formed of macromolecular assemblies of the disease-associated prion protein PrP(Sc), a misfolded isoform of the host-encoded prion protein PrP(C). Within defined host-species, prions can exist as conformational variants or strains. Based on both the M/V polymorphism at codon 129 of PrP and the electrophoretic signature of PrP(Sc) in the brain, sporadic CJD is classified in different subtypes, which may encode different strains. A transmission barrier, the mechanism of which remains unknown, limits prion cross-species propagation. To adapt to the new host, prions have the capacity to 'mutate' conformationally, leading to the emergence of a variant with new biological properties. Here, we transmitted experimentally one rare subtype of human CJD, designated cortical MM2 (129 MM with type 2 PrP(Sc)), to transgenic mice overexpressing either human or the VRQ allele of ovine PrP(C). In marked contrast with the reported absence of transmission to knock-in mice expressing physiological levels of human PrP, this subtype transmitted faithfully to mice overexpressing human PrP, and exhibited unique strain features. Onto the ovine PrP sequence, the cortical MM2 subtype abruptly evolved on second passage, thereby allowing emergence of a pair of strain variants with distinct PrP(Sc) biochemical characteristics and differing tropism for the central and lymphoid tissues. These two strain components exhibited remarkably distinct replicative properties in cell-free amplification assay, allowing the 'physical' cloning of the minor, lymphotropic component, and subsequent isolation in ovine PrP mice and RK13 cells. Here, we provide in-depth assessment of the transmissibility and evolution of one rare subtype of

Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins.

Science.gov (United States)

Bondy-Denomy, Joseph; Garcia, Bianca; Strum, Scott; Du, Mingjian; Rollins, MaryClare F; Hidalgo-Reyes, Yurima; Wiedenheft, Blake; Maxwell, Karen L; Davidson, Alan R

2015-10-01

The battle for survival between bacteria and the viruses that infect them (phages) has led to the evolution of many bacterial defence systems and phage-encoded antagonists of these systems. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated (cas) genes comprise an adaptive immune system that is one of the most widespread means by which bacteria defend themselves against phages. We identified the first examples of proteins produced by phages that inhibit a CRISPR-Cas system. Here we performed biochemical and in vivo investigations of three of these anti-CRISPR proteins, and show that each inhibits CRISPR-Cas activity through a distinct mechanism. Two block the DNA-binding activity of the CRISPR-Cas complex, yet do this by interacting with different protein subunits, and using steric or non-steric modes of inhibition. The third anti-CRISPR protein operates by binding to the Cas3 helicase-nuclease and preventing its recruitment to the DNA-bound CRISPR-Cas complex. In vivo, this anti-CRISPR can convert the CRISPR-Cas system into a transcriptional repressor, providing the first example-to our knowledge-of modulation of CRISPR-Cas activity by a protein interactor. The diverse sequences and mechanisms of action of these anti-CRISPR proteins imply an independent evolution, and foreshadow the existence of other means by which proteins may alter CRISPR-Cas function.

Modeling back-relaxation in ionic polymer metal composites: The role of steric effects and composite layers

Science.gov (United States)

Porfiri, Maurizio; Sharghi, Hesam; Zhang, Peng

2018-01-01

Ionic polymer metal composites (IPMCs) are a new class of active materials that are gaining traction as soft actuators in medical and industrial applications. IPMCs can undergo large deformations under modest voltage inputs, in dry and wet environments. Past studies have demonstrated that physical and geometric properties of all the IPMC constituents (ionomer, electrodes, and counterions) may all influence the time scales of the transient response and severity of the back-relaxation. In this study, we present a detailed mathematical model to investigate how the finite size of the counterions and the presence of metal particles in the vicinity of the electrodes modulate IPMC actuation. We build on previous work by our group on thermodynamically consistent modeling of IPMC mechanics and electrochemistry, which attributes IPMC actuation to the interplay between Maxwell stress and osmotic forces. To gain insight into the role of physical and geometric parameters, the resulting nonlinear partial differential equations are solved semianalytically using the method of matched asymptotic expansions, for the initial transient and the steady-state. A numerical solution in COMSOL Multiphysics® is developed to verify semianalytical findings and further explore IPMC actuation. Our model can successfully predict the entire response of IPMCs, from the initial bending toward the anode to the steady-state toward the cathode. We find that the steric effect can abolish the back-relaxation of IPMCs by restraining the counterions' concentration near the electrodes. We also find that increasing the thickness of the ionomer-metal composite layers may enhance IPMC actuation through increased osmotic forces and Maxwell stress.

Evaluation of mechanical strengths of three types of mini-implants in artificial bones

Directory of Open Access Journals (Sweden)

Yu-Chuan Tseng

2017-02-01

Full Text Available We investigates the effect of the anchor area on the mechanical strengths of infrazygomatic mini-implants. Thirty mini-implants were divided into three types based on the material and shape: Type A (titanium alloy, 2.0×12 mm, Type B (stainless steel, 2.0×12 mm, and Type C (titanium alloy, 2.0×11 mm.The mini-implants were inserted at 90° and 45° into the artificial bone to a depth of 7 mm, without predrilling. The mechanical strengths [insertion torque (IT, resonance frequency (RF, and removal torque (RT] and the anchor area were measured. We hypothesized that no correlation exists among the mechanical forces of each brand. In the 90° tests, the IT, RF, and RT of Type C (8.5 N cm, 10.2 kHz, and 6.1 N cm, respectively were significantly higher than those of Type A (5.0 N cm, 7.7 kHz, and 4.7 N cm, respectively. In the 45° test, the RFs of Type C (9.2 kHz was significantly higher than those of Type A (7.0 kHz and Type B (6.7 kHz. The anchor area of the mini-implants was in the order of Type C (706 mm2>Type B (648 mm2>Type A (621 mm2. Type C exhibited no significant correlation in intragroup comparisons, and the hypothesis was accepted. In the 90° and 45° tests, Type C exhibited the largest anchor area and the highest mechanical strengths (IT, RF, and RT among the three types of mini-implants. The anchor area plays a crucial role in the mechanical strength of mini-implants.

Evaluation of mechanical strengths of three types of mini-implants in artificial bones.

Science.gov (United States)

Tseng, Yu-Chuan; Wu, Ju-Hui; Ting, Chun-Chan; Chen, Hong-Sen; Chen, Chun-Ming

2017-02-01

We investigates the effect of the anchor area on the mechanical strengths of infrazygomatic mini-implants. Thirty mini-implants were divided into three types based on the material and shape: Type A (titanium alloy, 2.0×12 mm), Type B (stainless steel, 2.0×12 mm), and Type C (titanium alloy, 2.0×11 mm).The mini-implants were inserted at 90° and 45° into the artificial bone to a depth of 7 mm, without predrilling. The mechanical strengths [insertion torque (IT), resonance frequency (RF), and removal torque (RT)] and the anchor area were measured. We hypothesized that no correlation exists among the mechanical forces of each brand. In the 90° tests, the IT, RF, and RT of Type C (8.5 N cm, 10.2 kHz, and 6.1 N cm, respectively) were significantly higher than those of Type A (5.0 N cm, 7.7 kHz, and 4.7 N cm, respectively). In the 45° test, the RFs of Type C (9.2 kHz) was significantly higher than those of Type A (7.0 kHz) and Type B (6.7 kHz). The anchor area of the mini-implants was in the order of Type C (706 mm 2 )>Type B (648 mm 2 )>Type A (621 mm 2 ). Type C exhibited no significant correlation in intragroup comparisons, and the hypothesis was accepted. In the 90° and 45° tests, Type C exhibited the largest anchor area and the highest mechanical strengths (IT, RF, and RT) among the three types of mini-implants. The anchor area plays a crucial role in the mechanical strength of mini-implants. Copyright © 2016. Published by Elsevier Taiwan.

Search strange (S = -2) dibaryons in the reaction K-+d->K++MM at 1,4 GeV/c

International Nuclear Information System (INIS)

D'Agostini, G.; Auriemma, G.; Marini, G.; Martellotti, G.; Massa, F.; Nigro, A.; Rambaldi, A.; Sciubba, A.

1982-01-01

The reaction K - + d -> K + + MM has been studied at 1.4 GeV/c, to search for Q = -1, S = -2 dibaryonic states, in the mass range approx.= 2.1-2.5 GeV/c 2 . No evidence for the presence of structures has been found and upper limits for the backward production differential cross section for narrow states are established. (orig.)

13C nuclear magnetic resonance data of lanosterol derivatives—Profiling the steric topology of the steroid skeleton via substituent effects on its 13C NMR

Science.gov (United States)

Dias, Jerry Ray; Gao, Hongwu

2009-12-01

The 13C NMR spectra of over 24 tetracyclic triterpenoid derivatives have been structurally analyzed. The 13C NMR chemical shifts allow one to probe the steric topology of the rigid steroid skeleton and inductive effects of its substituents. Use of deuterium labeling in chemical shift assignment and B-ring aromatic terpenoids are also featured.

Thermochemical Erosion Modeling of the 25-MM M242/M791 Gun System

National Research Council Canada - National Science Library

Sopok, Samuel

1997-01-01

The MACE gun barrel thermochemical erosion modeling code addresses wall degradations due to transformations, chemical reactions, and cracking coupled with pure mechanical erosion for the 25-mm M242/M791 gun system...

TEM characterization of Al-C-Cu-Al2O3 composites produced by mechanical milling

International Nuclear Information System (INIS)

Santos-Beltran, A.; Gallegos-Orozco, V.; Estrada-Guel, I.; Bejar-Gomez, L.; Espinosa-Magana, F.; Miki-Yoshida, M.; Martinez-Sanchez, R.

2007-01-01

Novel Al-based composites (Al-C-Cu-Al 2 O 3 ) obtained by mechanical milling (MM), were characterized by transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Analyses of composites were carried out in both, the as-milled and the as-sintered conditions. C nanoparticles were found in the as-milled condition and Al 2 O 3 nanofibers were found in as-sintered products, as determined by EELS. C and Cu react with Al to crystallize in Al 3 C 4 and Al 2 Cu structures, respectively

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Science.gov (United States)

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

Characterization of a 6×6-mm{sup 2} 75-μm cell MPPC suitable for the Cherenkov Telescope Array project

Energy Technology Data Exchange (ETDEWEB)

Romeo, G., E-mail: giuseppe.romeo@oact.inaf.it [INAF, Osservatorio Astrofisico di Catania, Via S. Sofia 78, I-95123 Catania (Italy); Bonanno, G.; Garozzo, S.; Grillo, A.; Marano, D.; Munari, M.; Timpanaro, M.C. [INAF, Osservatorio Astrofisico di Catania, Via S. Sofia 78, I-95123 Catania (Italy); Catalano, O.; Giarrusso, S.; Impiombato, D.; La Rosa, G.; Sottile, G. [INAF, Istituto di Astrofisica Spaziale e Fisica cosmica di Palermo, Via U. La Malfa 153, I-90146 Palermo (Italy)

2016-08-01

This paper presents the latest characterization results of a novel Low Cross-Talk (LCT) large-area (6×6-mm{sup 2}) Multi-Pixel Photon Counter (MPPC) detector manufactured by Hamamatsu, belonging to the recent LCT5 family and achieving a fill-factor enhancement and cross-talk reduction. In addition, the newly adopted resin coating is demonstrated to yield improved photon detection capabilities in the 290–350 nm spectral range, making the new LCT MPPC particularly suitable for emerging applications like Cherenkov Telescopes. For a 3×3-mm{sup 2} version of the new MPPC under test, a comparative analysis of the large pixel pitch (75-µm) detector versus the smaller pixel pitch (50-µm) detector is also undertaken. Furthermore, measurements of the 6×6-mm{sup 2} MPPC response versus the angle of incidence are provided for the characterized device.

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

Science.gov (United States)

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Growth Mechanism of Microbial Colonies

Science.gov (United States)

Zhu, Minhui; Martini, K. Michael; Kim, Neil H.; Sherer, Nicholas; Lee, Jia Gloria; Kuhlman, Thomas; Goldenfeld, Nigel

Experiments on nutrient-limited E. coli colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. Supported by NSF Grant 0822613.

Molecular mechanisms and in vitro antioxidant effects of Lactobacillus plantarum MA2.

Science.gov (United States)

Tang, Wei; Xing, Zhuqing; Li, Chao; Wang, Jinju; Wang, Yanping

2017-04-15

Lactobacillus plantarum MA2 was isolated from Chinese traditional Tibetan kefir grains. The antioxidant activities in vitro of this strain were evaluated extensively. The results showed that L. plantarum MA2 can tolerate hydrogen peroxide up to 2.0mM, and its fermentate (fermented supernatant, intact cell and cell-free extract) had strong reducing capacities, lipid peroxidation inhibition capacities, Fe 2+ -chelating abilities, as well as various free radical scavenging capacities. Additionally, both the fermented supernatant and cell homogenate exhibited glutathione peroxidase activity and superoxide dismutase activity. In order to investigate the antioxidant mechanism of L. plantarum MA2 at the molecular level, eight antioxidant-related genes were identified, and further analyzed. Three groups of genes cat, gshR and npx, were found up-regulated under H 2 O 2 challenge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of Processed Nerve Allografts to Repair Nerve Injuries Greater Than 25 mm in the Hand.

Science.gov (United States)

Rinker, Brian; Zoldos, Jozef; Weber, Renata V; Ko, Jason; Thayer, Wesley; Greenberg, Jeffrey; Leversedge, Fraser J; Safa, Bauback; Buncke, Gregory

2017-06-01

Processed nerve allografts (PNAs) have been demonstrated to have improved clinical results compared with hollow conduits for reconstruction of digital nerve gaps less than 25 mm; however, the use of PNAs for longer gaps warrants further clinical investigation. Long nerve gaps have been traditionally hard to study because of low incidence. The advent of the RANGER registry, a large, institutional review board-approved, active database for PNA (Avance Nerve Graft; AxoGen, Inc, Alachua, FL) has allowed evaluation of lower incidence subsets. The RANGER database was queried for digital nerve repairs of 25 mm or greater. Demographics, injury, treatment, and functional outcomes were recorded on standardized forms. Patients younger than 18 and those lacking quantitative follow-up data were excluded. Recovery was graded according to the Medical Research Council Classification for sensory function, with meaningful recovery defined as S3 or greater level. Fifty digital nerve injuries in 28 subjects were included. There were 22 male and 6 female subjects, and the mean age was 45. Three patients gave a previous history of diabetes, and there were 6 active smokers. The most commonly reported mechanisms of injury were saw injuries (n = 13), crushing injuries (n = 9), resection of neuroma (n = 9), amputation/avulsions (n = 8), sharp lacerations (n = 7), and blast/gunshots (n = 4). The average gap length was 35 ± 8 mm (range, 25-50 mm). Recovery to the S3 or greater level was reported in 86% of repairs. Static 2-point discrimination (s2PD) and Semmes-Weinstein monofilament (SWF) were the most common completed assessments. Mean s2PD in 24 repairs reporting 2PD data was 9 ± 4 mm. For the 38 repairs with SWF data, protective sensation was reported in 33 repairs, deep pressure in 2, and no recovery in 3. These data compared favorably with historical data for nerve autograft repairs, with reported levels of meaningful recovery of 60% to 88%. There were no reported adverse effects

Mineralogic Model (MM3.0) Analysis Model Report

Energy Technology Data Exchange (ETDEWEB)

C. Lum

2002-02-12

) Geologic Framework Model (GFM); (2) Rock Properties Model (RPM); and (3) Mineralogic Model (MM). The ISM merges the detailed stratigraphy and structural features of the site into a 3-D model that will be useful in primary downstream models and repository design. These downstream models include the hydrologic flow models and the radionuclide transport models. All the models and the repository design, in turn, will be incorporated into the Total System Performance Assessment (TSPA) of the potential nuclear waste repository block and vicinity to determine the suitability of Yucca Mountain as a host for a repository. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 1. The lateral boundaries of the ISM and its three component models are shown in Figure 2.

Mineralogic Model (MM3.0) Analysis Model Report

International Nuclear Information System (INIS)

Lum, C.

2002-01-01

: (1) Geologic Framework Model (GFM); (2) Rock Properties Model (RPM); and (3) Mineralogic Model (MM). The ISM merges the detailed stratigraphy and structural features of the site into a 3-D model that will be useful in primary downstream models and repository design. These downstream models include the hydrologic flow models and the radionuclide transport models. All the models and the repository design, in turn, will be incorporated into the Total System Performance Assessment (TSPA) of the potential nuclear waste repository block and vicinity to determine the suitability of Yucca Mountain as a host for a repository. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 1. The lateral boundaries of the ISM and its three component models are shown in Figure 2

450mm wafer patterning with jet and flash imprint lithography

Science.gov (United States)

Thompson, Ecron; Hellebrekers, Paul; Hofemann, Paul; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2013-09-01

The next step in the evolution of wafer size is 450mm. Any transition in sizing is an enormous task that must account for fabrication space, environmental health and safety concerns, wafer standards, metrology capability, individual process module development and device integration. For 450mm, an aggressive goal of 2018 has been set, with pilot line operation as early as 2016. To address these goals, consortiums have been formed to establish the infrastructure necessary to the transition, with a focus on the development of both process and metrology tools. Central to any process module development, which includes deposition, etch and chemical mechanical polishing is the lithography tool. In order to address the need for early learning and advance process module development, Molecular Imprints Inc. has provided the industry with the first advanced lithography platform, the Imprio® 450, capable of patterning a full 450mm wafer. The Imprio 450 was accepted by Intel at the end of 2012 and is now being used to support the 450mm wafer process development demands as part of a multi-year wafer services contract to facilitate the semiconductor industry's transition to lower cost 450mm wafer production. The Imprio 450 uses a Jet and Flash Imprint Lithography (J-FILTM) process that employs drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for markets including NAND Flash memory, patterned media for hard disk drives and displays. This paper reviews the recent performance of the J-FIL technology (including overlay, throughput and defectivity), mask development improvements provided by Dai Nippon Printing, and the application of the technology to a 450mm lithography platform.

Comparison Study of Percutaneous Osseointegrated Bone Conduction Device Complications When Using the 9 mm Abutment Versus 6 mm Abutment at Initial Implantation.

Science.gov (United States)

Wise, Sean R; LaRouere, Jacqueline S; Bojrab, Dennis I; LaRouere, Michael J

2018-04-01

To assess differences in the incidence, type, and management of complications encountered with implantation of percutaneous osseointegrated bone conduction devices when using a 9 mm abutment versus 6 mm abutment at initial implantation. Retrospective cohort study. One hundred thirty consecutive patients between January 2010 and December 2011 underwent single-stage percutaneous osseointegrated bone conduction device implantation using a 9 or 6 mm abutment. Clinical outcomes assessed for the two groups included the incidence, type, and management of postoperative complications. Abutment size, age, sex, indication for surgery, implant device type, duration of follow-up, and patient comorbidities were evaluated as potential factors affecting outcomes. Average duration of follow-up was 16 months (range 6-29 mo). Postoperative complications occurred in 38 (29.2%) patients. Twenty-four (18.4%) patients experienced minor complications requiring simple, local care; eight (6.1%) patients required in-office procedural intervention; and six (4.6%) patients required revision surgery in the operating room. Implant extrusion occurred in three (2.3%) patients. Eleven (8.5%) patients required placement of a longer abutment. Patients receiving the 6 mm abutment at initial surgery were significantly more likely to encounter a complication requiring in-office procedural intervention or revision surgery (p = 0.001). Minor complications after implantation of percutaneous osseointegrated bone conduction devices are common. The vast majority of these complications are due to localized skin reactions, most of which are readily addressed through local care. Patients receiving the 9 mm abutment during initial implantation are significantly less likely to require in-office procedural intervention or revision surgery postoperatively as compared with those receiving the shorter, 6 mm abutment.

J e (4.2?K, 31.2 T) beyond 1?kA/mm2 of a ~3.2??m thick, 20?mol% Zr-added MOCVD REBCO coated conductor

OpenAIRE

Xu, A.; Zhang, Y.; Gharahcheshmeh, M. Heydari; Yao, Y.; Galstyan, E.; Abraimov, D.; Kametani, F.; Polyanskii, A.; Jaroszynski, J.; Griffin, V.; Majkic, G.; Larbalestier, D. C.; Selvamanickam, V.

2017-01-01

A main challenge that significantly impedes REBa2Cu3Ox (RE?=?rare earth) coated conductor applications is the low engineering critical current density J e because of the low superconductor fill factor in a complicated layered structure that is crucial for REBa2Cu3Ox to carry supercurrent. Recently, we have successfully achieved engineering critical current density beyond 2.0?kA/mm2 at 4.2?K and 16 T, by growing thick REBa2Cu3Ox layer, from ?1.0??m up to ?3.2??m, as well as controlling the pin...

20th CISM-IFToMM Symposium on Theory and Practice of Robots and Manipulators

CERN Document Server

Glazunov, Victor

2014-01-01

This proceedings volume contains papers that have been selected after review for oral presentation at ROMANSY 2014, the 20th CISM-IFToMM Symposium on Theory and Practice of Robots and Manipulators. These papers cover advances on several aspects of the wide field of Robotics as concerning Theory and Practice of Robots and Manipulators. ROMANSY 2014 is the twentieth event in a series that started in 1973 as one of the first conference activities in the world on Robotics. The first event was held at CISM (International Centre for Mechanical Science) in Udine, Italy on 5-8 September 1973. It was also the first topic conference of IFToMM (International Federation for the Promotion of Mechanism and Machine Science) and it was directed not only to the IFToMM community. Proceedings volumes of ROMANSY have been always published to be available, also after the symposium, to a large public of scholars and designers with the aim to give an overview of new advances and trends in the theory, design, and practice of robots....

Lesion of the commissural nucleus of the solitary tract/A2 noradrenergic neurons facilitates the activation of angiotensinergic mechanisms in response to hemorrhage.

Science.gov (United States)

Freiria-Oliveira, A H; Blanch, G T; De Paula, P M; Menani, J V; Colombari, D S A

2013-12-19

In the present study, we investigated the effects of lesions of A2 neurons of the commissural nucleus of the solitary tract (cNTS) alone or combined with the blockade of angiotensinergic mechanisms on the recovery of arterial pressure (AP) to hemorrhage in conscious rats. Male Holtzman rats (280-320g) received an injection of anti-dopamine-beta-hydroxylase-saporin (12.6ng/60nl; cNTS/A2-lesion, n=28) or immunoglobulin G (IgG)-saporin (12.6ng/60nl, sham, n=24) into the cNTS and 15-21days later had a stainless steel cannula implanted in the lateral ventricle. After 6days, rats were submitted to hemorrhage (four blood withdrawals, 2ml/300g of body weight every 10min). Both cNTS/A2-lesioned and sham rats had similar hypotension to hemorrhage (-62±7 and -73±7mmHg, respectively), however cNTS/A2-lesioned rats rapidly recovered from hypotension (-5±3mmHg at 30min), whereas sham rats did not completely recover until the end of the recording (-20±3mmHg at 60min). Losartan (angiotensin type 1 receptor antagonist) injected intracerebroventricularly (100μg/1μl) or intravenously (i.v.) (10mg/kg of body weight) impaired the recovery of AP in cNTS/A2-lesioned rats (-24±6 and -35±7mmHg at 30min, respectively). In sham rats, only i.v. losartan affected the recovery of AP (-39±6mmHg at 60min). The results suggest that lesion of the A2 neurons in the cNTS facilitates the activation of the angiotensinergic pressor mechanisms in response to hemorrhage. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

Synthesis and computer-aided structural investigation of potentially photochromic spirooxazines

International Nuclear Information System (INIS)

Chi, L.

2000-03-01

Quantum mechanical methods, PPP-MO and ZINDO, were used to predict the electronic spectra of the ring-opened forms and ring-closed forms respectively of a series of spirooxazines. Molecular mechanics was used to optimise the molecular geometry and to calculate the molecular final energy (steric energy) using the MM2 force field method. An all-valence-electron quantum mechanical method was employed to calculate the heats of formation using AM1 parameters, and the data were used to provide a measure of the stability of the molecules. This computer-aided structural investigation has provided an enhanced understanding of the spirooxazine system and methods with the potential to predict photochromic behaviour have emerged. The synthesis of a series of heterocyclic analogues of the well-known spironaphthoxazines based on quinolines, coumarin and pyrazolones were attempted. The properties of the compounds obtained were correlated with the results of the calculations. (author)

Simulation of Thermal Processes in Metamaterial MM-to-IR Converter for MM-wave Imager

International Nuclear Information System (INIS)

Zagubisalo, Peter S; Paulish, Andrey G; Kuznetsov, Sergey A

2014-01-01

The main characteristics of MM-wave image detector were simulated by means of accurate numerical modelling of thermophysical processes in a metamaterial MM-to-IR converter. The converter represents a multilayer structure consisting of an ultra thin resonant metamaterial absorber and a perfect emissive layer. The absorber consists of a dielectric self-supporting film that is metallized from both sides. A micro-pattern is fabricated from one side. Resonant absorption of the MM waves induces the converter heating that yields enhancement of IR emission from the emissive layer. IR emission is detected by IR camera. In this contribution an accurate numerical model for simulation of the thermal processes in the converter structure was created by using COMSOL Multiphysics software. The simulation results are in a good agreement with experimental results that validates the model. The simulation shows that the real time operation is provided for the converter thickness less than 3 micrometers and time response can be improved by decreasing of the converter thickness. The energy conversion efficiency of MM waves into IR radiation is over 80%. The converter temperature increase is a linear function of a MM-wave radiation power within three orders of the dynamic range. The blooming effect and ways of its reducing are also discussed. The model allows us to choose the ways of converter structure optimization and improvement of image detector parameters

Microstructure and mechanical properties of 2.5 vol. % TiBw/Ti6Al4V composites plates fabricated by hot-hydrostatic canned extrusion

Science.gov (United States)

Zhang, Wencong; Zhang, Lingjia; Feng, Yangju; Cui, Guorong; Chen, Wenzhen

2018-04-01

Plates of 2.5 vol. % TiB whisker-reinforced Ti6Al4V titanium matrix composites (TiBw/Ti64) with network structure were successfully fabricated by hot-hydrostatic extrusion with steel cup at 1100 °C. The dimensions of plates were about 150mm in length, 27mm in width and 2mm in thickness. After extrusion, the original equiaxed-network structure formed by TiB whiskers still existed, but was compressed in cross-section and stretched in longitudinal section and then the TiB whiskers were directional distribution along the extrusion direction. Furthermore, the mechanical properties results showed that the strength, hardness and ductility of the plates were significantly improved compared to as-sintered composites.

Atropisomerism about aryl-Csp(3) bonds: the electronic and steric influence of ortho-substituents on conformational exchange in cannabidiol and linderatin derivatives.

Science.gov (United States)

Berber, Hatice; Lameiras, Pedro; Denhez, Clément; Antheaume, Cyril; Clayden, Jonathan

2014-07-03

Terpenylation reactions of substituted phenols were used to prepare cannabidiol and linderatin derivatives, and their structure and conformational behavior in solution were investigated by NMR and, for some representative examples, by DFT. VT-NMR spectra and DFT calculations were used to determine the activation energies of the conformational change arising from restricted rotation about the aryl-Csp(3) bond that lead to two unequally populated rotameric epimers. The NBO calculation was applied to explain the electronic stabilization of one conformer over another by donor-acceptor charge transfer interactions. Conformational control arises from a combination of stereoelectronic and steric effects between substituents in close contact with each other on the two rings of the endocyclic epoxide atropisomers. This study represents the first exploration of the stereoelectronic origins of atropisomerism around C(sp(2))-C(sp(3)) single bonds through theoretical calculations.

An M/M/2 Queueing System with Heterogeneous Servers Including One with Working Vacation

Directory of Open Access Journals (Sweden)

A. Krishnamoorthy

2012-01-01

Full Text Available This paper analyzes an M/M/2 queueing system with two heterogeneous servers, one of which is always available but the other goes on vacation in the absence of customers waiting for service. The vacationing server, however, returns to serve at a low rate as an arrival finds the other server busy. The system is analyzed in the steady state using matrix geometric method. Busy period of the system is analyzed and mean waiting time in the stationary regime computed. Conditional stochastic decomposition of stationary queue length is obtained. An illustrative example is also provided.

Atomic layer deposition of two dimensional MoS{sub 2} on 150 mm substrates

Energy Technology Data Exchange (ETDEWEB)

Valdivia, Arturo; Conley, John F., E-mail: jconley@eecs.oregonstate.edu [School of EECS, Oregon State University, Corvallis, Oregon 97331 (United States); Tweet, Douglas J. [Sharp Labs of America, Camas, Washington 98607 (United States)

2016-03-15

Low temperature atomic layer deposition (ALD) of monolayer to few layer MoS{sub 2} uniformly across 150 mm diameter SiO{sub 2}/Si and quartz substrates is demonstrated. Purge separated cycles of MoCl{sub 5} and H{sub 2}S precursors are used at reactor temperatures of up to 475 °C. Raman scattering studies show clearly the in-plane (E{sup 1}{sub 2g}) and out-of-plane (A{sub 1g}) modes of MoS{sub 2}. The separation of the E{sup 1}{sub 2g} and A{sub 1g} peaks is a function of the number of ALD cycles, shifting closer together with fewer layers. X-ray photoelectron spectroscopy indicates that stoichiometry is improved by postdeposition annealing in a sulfur ambient. High resolution transmission electron microscopy confirms the atomic spacing of monolayer MoS{sub 2} thin films.

A highly sensitive and selective fluorescent sensor for detection of sulfide anion based on the steric hindrance effect

Science.gov (United States)

Chen, Guanfan; Tang, Mengzhuo; Fu, Xiufang; Cheng, Fenmin; Zou, Xianghua; Wang, Jingpei; Zeng, Rongjin

2018-01-01

Sulfide anions are not only generated as a byproduct from industrial processes but also as a crucial kind of element in biological systems. Therefore, fluorescent probes for detecting sulfide anion with sensitive and selective characters are highly popular. In this study, we report a highly sensitive and selective fluorescent sensor M1 for detection of sulfide anion based on the steric hindrance effect, where the recognition unit, dinitrobenzenesulfonate ester group is linked to aromatic ortho-position in the porphyrin, and correspondingly the fluorescence of fluorescein is efficiently quenched. Compared with the sensors with recognition unit linked to the other aromatic positions, the fluorescent sensor M1 has a lower fluorescence background. Furthermore, the corresponding fluorescence responses (F/F0) of M1 for mercapto amino-acid GSH, Hcy and Cys, were all far lower than the relative fluorescence ratio F/F0 values for S2-. It means that M1 is sensitive and selective to detection of S2-, and has an anti-disturbance ability to the biologically-relevant thiols, GSH, Hcy and Cys, and has the prospect of application in the exact detection of sulfide anions in living organisms. This approach offers some useful insights for realizing sensitive and selective fluorescent turn-on sensing in the detection assays for other analytes.

Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies

Energy Technology Data Exchange (ETDEWEB)

Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

2009-03-01

Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for propercomputational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an

Assessments of Ali, Dome A, and Summit Camp for mm-wave Observations Using MERRA-2 Reanalysis

Science.gov (United States)

Kuo, Chao-Lin

2017-10-01

NASA’s latest MERRA-2 reanalysis of the modern satellite measurements has made atmospheric data easily accessible with unprecedented uniformity, fidelity, and completeness. In this paper, these data are used to evaluate five sites for millimeter-wave (mm-wave) observations. These include two established sites (South Pole and Chajnantor, Atacama), and three new sites (Ali in Tibet, Dome A in Antarctica, and Summit Camp in Greenland). Atmospheric properties including precipitable water vapor (PWV), sky brightness temperature fluctuations, and ice and liquid water paths are derived and compared. Dome A emerges to be the best among those evaluated, with PWV and fluctuations smaller than the second-best site, South Pole, by more than a factor of 2. It is found that the higher site in Ali (6100 m) is on par with Cerro Chajnantor (5612 m) in terms of transmission and stability. The lower site in Ali (5250 m) planned for the first stage of observations at 90/150 GHz provides conditions comparable to those on the Chajnantor Plateau. These analyses confirm Ali to be an excellent mm-wave site in the Northern Hemisphere that will complement well-established Southern sites. According to MERRA-2 data, the observing conditions at Summit Camp are also comparable to Cerro Chajnantor. However, it is more affected by the presence of liquid water clouds.

Assessments of Ali, Dome A, and Summit Camp for mm-wave Observations Using MERRA-2 Reanalysis

International Nuclear Information System (INIS)

Kuo, Chao-Lin

2017-01-01

NASA's latest MERRA-2 reanalysis of the modern satellite measurements has made atmospheric data easily accessible with unprecedented uniformity, fidelity, and completeness. In this paper, these data are used to evaluate five sites for millimeter-wave (mm-wave) observations. These include two established sites (South Pole and Chajnantor, Atacama), and three new sites (Ali in Tibet, Dome A in Antarctica, and Summit Camp in Greenland). Atmospheric properties including precipitable water vapor (PWV), sky brightness temperature fluctuations, and ice and liquid water paths are derived and compared. Dome A emerges to be the best among those evaluated, with PWV and fluctuations smaller than the second-best site, South Pole, by more than a factor of 2. It is found that the higher site in Ali (6100 m) is on par with Cerro Chajnantor (5612 m) in terms of transmission and stability. The lower site in Ali (5250 m) planned for the first stage of observations at 90/150 GHz provides conditions comparable to those on the Chajnantor Plateau. These analyses confirm Ali to be an excellent mm-wave site in the Northern Hemisphere that will complement well-established Southern sites. According to MERRA-2 data, the observing conditions at Summit Camp are also comparable to Cerro Chajnantor. Furthermore, it is more affected by the presence of liquid water clouds.

Metal-Free CVD Graphene Synthesis on 200 mm Ge/Si(001) Substrates.

Science.gov (United States)

Lukosius, M; Dabrowski, J; Kitzmann, J; Fursenko, O; Akhtar, F; Lisker, M; Lippert, G; Schulze, S; Yamamoto, Y; Schubert, M A; Krause, H M; Wolff, A; Mai, A; Schroeder, T; Lupina, G

2016-12-14

Good quality, complementary-metal-oxide-semiconductor (CMOS) technology compatible, 200 mm graphene was obtained on Ge(001)/Si(001) wafers in this work. Chemical vapor depositions were carried out at the deposition temperatures of 885 °C using CH 4 as carbon source on epitaxial Ge(100) layers, which were grown on Si(100), prior to the graphene synthesis. Graphene layer with the 2D/G ratio ∼3 and low D mode (i.e., low concentration of defects) was measured over the entire 200 mm wafer by Raman spectroscopy. A typical full-width-at-half-maximum value of 39 cm -1 was extracted for the 2D mode, further indicating that graphene of good structural quality was produced. The study also revealed that the lack of interfacial oxide correlates with superior properties of graphene. In order to evaluate electrical properties of graphene, its 2 × 2 cm 2 pieces were transferred onto SiO 2 /Si substrates from Ge/Si wafers. The extracted sheet resistance and mobility values of transferred graphene layers were ∼1500 ± 100 Ω/sq and μ ≈ 400 ± 20 cm 2 /V s, respectively. The transferred graphene was free of metallic contaminations or mechanical damage. On the basis of results of DFT calculations, we attribute the high structural quality of graphene grown by CVD on Ge to hydrogen-induced reduction of nucleation probability, explain the appearance of graphene-induced facets on Ge(001) as a kinetic effect caused by surface step pinning at linear graphene nuclei, and clarify the orientation of graphene domains on Ge(001) as resulting from good lattice matching between Ge(001) and graphene nucleated on such nuclei.

Combined quantum mechanical and molecular mechanical method for metal-organic frameworks: proton topologies of NU-1000.

Science.gov (United States)

Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

2018-01-17

Metal-organic frameworks (MOFs) are materials with applications in catalysis, gas separations, and storage. Quantum mechanical (QM) calculations can provide valuable guidance to understand and predict their properties. In order to make the calculations faster, rather than modeling these materials as periodic (infinite) systems, it is useful to construct finite models (called cluster models) and use subsystem methods such as fragment methods or combined quantum mechanical and molecular mechanical (QM/MM) methods. Here we employ a QM/MM methodology to study one particular MOF that has been of widespread interest because of its wide pores and good solvent and thermal stability, namely NU-1000, which contains hexanuclear zirconium nodes and 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy 4- ) linkers. A modified version of the Bristow-Tiana-Walsh transferable force field has been developed to allow QM/MM calculations on NU-1000; we call the new parametrization the NU1T force field. We consider isomeric structures corresponding to various proton topologies of the [Zr 6 (μ 3 -O) 8 O 8 H 16 ] 8+ node of NU-1000, and we compute their relative energies using a QM/MM scheme designed for the present kind of problem. We compared the results to full quantum mechanical (QM) energy calculations and found that the QM/MM models can reproduce the full QM relative energetics (which span a range of 334 kJ mol -1 ) with a mean unsigned deviation (MUD) of only 2 kJ mol -1 . Furthermore, we found that the structures optimized by QM/MM are nearly identical to their full QM optimized counterparts.

[A case of MM1+2 Creutzfeldt-Jakob disease with a longitudinal study of EEG and MRI].

Science.gov (United States)

Katsube, Mizuho; Shiota, Yuri; Harada, Takayuki; Shibata, Hiroshi; Nagai, Atsushi

2013-11-01

We report a case of definite MM1 + 2 sporadic Creutzfeldt-Jakob disease (sCJD). A 66-year-old woman was admitted to our hospital with memory disturbance and disorientation for three months. On admission she presented a progressive cognitive insufficiency. Electroencephalography (EEG) revealed a frontal intermittent rhythmical delta activity (FIRDA) and the brain magnetic resonance imaging (MRI) showed high signal intensities in cerebral cortex on diffusion weighted images (DWI). After four months from the onset, she reached the akinetic mutism state followed by myoclonus. Follow up examination revealed that periodic synchronous discharge (PSD) was found in EEG, and DWI revealed enlargement of high signal intensity lesions in cerebral cortex. At seven months from the onset, PSD and high signal intensities of cortex became unclear with disappearance of myoclonus, and brain white matter lesions were evident on MRI. Serial studies of EEG and MRI revealed that PSD generalized from frontal lobe dominant pattern, while high signal intensity lesions of cortex diffusely increased on DWI. At ten months from the onset patient died. Pathological examination in brain showed moderate and diffuse neuronal cell loss and gliosis in cerebral cortex corresponding with DWI changes. The genotype at codon 129 of the prion protein (PrP) was homozygous methionine (MM) and the type of protease-resistant PrP (PrPres) was the mixed type of 1 and 2 in Western blot analysis. It has been rare to analyze the changes of EEG and MRI in the entire stage and to investigate pathological finding in the case of sCJD-MM1 + 2. A longitudinal examination of EEG and MRI is useful for early diagnosis of CJD. Also we could correlate these findings with clinical and histopathological phenotype.

Modification of Hack Saw Blade Support 'REMOR 400' from the Length of 650 mm to 450 mm

International Nuclear Information System (INIS)

Sagino, Abdul-Hafid

2005-01-01

REMOR 400 type is the hack saw machine for cutting large work piece. The capacity of cutting is 310 mm diameter. The length of the blade is 650 mm (26 inches). For cutting small work piece (≤ 150 mm), the use of this blade is not efficient because the blade is relatively expensive. To solve this problem, the modification of the blade support is performed so that REMOR 400 machine can use the blade of 450 mm which is cheaper and easier to find in the market. (author)

Mechanism of isotactic styrene polymerization with a C 6F 5-substituted bis(phenoxyimine) titanium system

KAUST Repository

Caporaso, Lucia; Loria, Marianna; Mazzeo, Mina; Michiue, Kenji; Nakano, Takashi; Fujita, Terunori; Cavallo, Luigi

2012-01-01

We report a combined, experimental and theoretical, study of styrene polymerization to clarify the regio- and stereocontrol mechanism operating with a C 6F 5-substituted bis(phenoxyimine) titanium dichloride complex. Styrene homopolymerization, styrene-propene and styrene-ethene-propene copolymerizations have been carried out to this aim. A combination of 13C NMR analysis of the chain-end groups and of the microstructure of the homopolymers and copolymers reveals that styrene polymerization is highly regioselective and occurs prevalently through 2,1-monomer insertion. DFT calculations evidenced that steric interaction between the growing chain and the monomer in the transition state insertion stage is at the origin of this selectivity. The formation of isotactic polystyrene with a chain-end like microstructure is rationalized on the base of a mechanism similar to that proposed for the syndiospecific propene polymerization catalyzed by bis(phenoxyimine) titanium dichloride complexes. Finally, a general stereocontrol mechanism operative in olefin polymerization with this class of complexes is proposed. © 2012 American Chemical Society.

Mechanism of isotactic styrene polymerization with a C 6F 5-substituted bis(phenoxyimine) titanium system

KAUST Repository

Caporaso, Lucia

2012-11-13

We report a combined, experimental and theoretical, study of styrene polymerization to clarify the regio- and stereocontrol mechanism operating with a C 6F 5-substituted bis(phenoxyimine) titanium dichloride complex. Styrene homopolymerization, styrene-propene and styrene-ethene-propene copolymerizations have been carried out to this aim. A combination of 13C NMR analysis of the chain-end groups and of the microstructure of the homopolymers and copolymers reveals that styrene polymerization is highly regioselective and occurs prevalently through 2,1-monomer insertion. DFT calculations evidenced that steric interaction between the growing chain and the monomer in the transition state insertion stage is at the origin of this selectivity. The formation of isotactic polystyrene with a chain-end like microstructure is rationalized on the base of a mechanism similar to that proposed for the syndiospecific propene polymerization catalyzed by bis(phenoxyimine) titanium dichloride complexes. Finally, a general stereocontrol mechanism operative in olefin polymerization with this class of complexes is proposed. © 2012 American Chemical Society.

Detection of 2-mm-long strained section in silica fiber using slope-assisted Brillouin optical correlation-domain reflectometry

Science.gov (United States)

Lee, Heeyoung; Mizuno, Yosuke; Nakamura, Kentaro

2018-02-01

Slope-assisted Brillouin optical correlation-domain reflectometry is a single-end-access distributed Brillouin sensing technique with high spatial resolution and high-speed operation. We have recently discovered its unique feature, that is, strained or heated sections even shorter than nominal resolution can be detected, but its detailed characterization has not been carried out. Here, after experimentally characterizing this “beyond-nominal-resolution” effect, we show its usefulness by demonstrating the detection of a 2-mm-long strained section along a silica fiber. We also demonstrate the detection of a 5-mm-long heated section along a polymer optical fiber. The lengths of these detected sections are smaller than those of the other demonstrations reported so far.

Friction and wear mechanisms in MoS2/Sb2O3/Au nanocomposite coatings

International Nuclear Information System (INIS)

Scharf, T.W.; Kotula, P.G.; Prasad, S.V.

2010-01-01

Fundamental phenomena governing the tribological mechanisms in sputter deposited amorphous MoS 2 /Sb 2 O 3 /Au nanocomposite coatings are reported. In dry environments the nanocomposite has the same low friction coefficient as pure MoS 2 (∼0.007). However, unlike pure MoS 2 coatings, which wear through in air (50% relative humidity), the composite coatings showed minimal wear, with wear factors of ∼1.2-1.4 x 10 -7 mm 3 Nm -1 in both dry nitrogen and air. The coatings exhibited non-Amontonian friction behavior, with the friction coefficient decreasing with increasing Hertzian contact stress. Cross-sectional transmission electron microscopy of wear surfaces revealed that frictional contact resulted in an amorphous to crystalline transformation in MoS 2 with 2H-basal (0 0 0 2) planes aligned parallel to the direction of sliding. In air the wear surface and subsurface regions exhibited islands of Au. The mating transfer films were also comprised of (0 0 0 2)-oriented basal planes of MoS 2 , resulting in predominantly self-mated 'basal on basal' interfacial sliding and, thus, low friction and wear.

Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study.

Science.gov (United States)

Zhang, Ruiming; Shi, Xiangli; Sun, Yanhui; Zhang, Qingzhu; Wang, Wenxing

2018-05-17

The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol -1 , respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB. Copyright © 2018. Published by Elsevier Ltd.

Radiological and micro-computed tomography analysis of the bone at dental implants inserted 2, 3 and 4 mm apart in a minipig model with platform switching incorporated.

Science.gov (United States)

Elian, Nicolas; Bloom, Mitchell; Dard, Michel; Cho, Sang-Choon; Trushkowsky, Richard D; Tarnow, Dennis

2014-02-01

The purpose of this study was to assess the effect of inter-implant distance on interproximal bone utilizing platform switching. Analysis of interproximal bone usually depends on traditional two-dimensional radiographic assessment. Although there has been increased reliability of current techniques, there has been an inability to track bone level changes over time and in three dimensions. Micro-CT has provided three-dimensional imaging that can be used in conjunction with traditional two-dimensional radiographic techniques. This study was performed on 24 female minipigs. Twelve animals received three implants with an inter-implant distance of 3 mm on one side of the mandible and another three implants on the contra-lateral side, where the implants were placed 2 mm apart creating a split mouth design. Twelve other animals received three implants with an inter-implant distance of 3 mm on one side of the mandible and another three implants on the contra-lateral side, where the implants were placed 4 mm apart creating a split mouth design too. The quantitative evaluation was performed comparatively on radiographs taken at t 0 (immediately after implantation) and at t 8 weeks (after termination). The samples were scanned by micro-computed tomography (μCT) to quantify the first bone to implant contact (fBIC) and bone volume/total volume (BV/TV). Mixed model regressions using the nonparametric Brunner-Langer method were used to determine the effect of inter-implant distance on the measured outcomes. The change in bone level was determined using radiography and its mean was 0.05 mm for an inter-implant distance of 3 and 0.00 mm for a 2 mm distance (P = 0.7268). The mean of this outcome was 0.18 mm for the 3 mm and for 4 mm inter-implant distance (P = 0.9500). Micro-computed tomography showed that the fBIC was always located above the reference, 0.27 and 0.20 mm for the comparison of 2-3 mm (P = 0.4622) and 0.49 and 0.34 mm for the inter-implant distance of 3 and 4 mm (P

MmWave Vehicle-to-Infrastructure Communication :Analysis of Urban Microcellular Networks

Science.gov (United States)

2017-05-01

Vehicle-to-infrastructure (V2I) communication may provide high data rates to vehicles via millimeterwave (mmWave) microcellular networks. This report uses stochastic geometry to analyze the coverage of urban mmWave microcellular networks. Prior work ...

Protective role of Nrf2 against mechanical-stretch-induced apoptosis in mouse fibroblasts: a potential therapeutic target of mechanical-trauma-induced stress urinary incontinence.

Science.gov (United States)

Li, Qiannan; Li, Bingshu; Liu, Cheng; Wang, Linlin; Tang, Jianming; Hong, Li

2018-01-10

We investigated the protective effect and underlying molecular mechanism of nuclear factor-E2-related factor 2 (Nrf2) against mechanical-stretch-induced apoptosis in mouse fibroblasts. Normal cells, Nrf2 silencing cells, and Nrf2 overexpressing cells were respectively divided into two groups-nonintervention and cyclic mechanical strain (CMS)-subjected to CMS of 5333 μ (1.0 Hz for 4 h), six groups in total (control, CMS, shNfe212, shNfe212 + CMS, LV-shNfe212, and LV-shNfe212 + CMS). After treatment, cell apoptosis; cell-cycle distribution; expressions of Nrf2, Bax, Bcl-2, Cyt-C, caspase-3, caspase-9, cleaved-caspase-3, and cleaved-caspase-9; mitochondrial membrane potential (ΔΨm); reactive oxygen species (ROS); and malondialdehyde (MDA) levels were measured. Thirty virgin female C57BL/6 mice were divided into two groups: control (without intervention) and vaginal distension (VD) groups, which underwent VD for 1 h with an 8-mm dilator (0.3 ml saline). Leak-point pressure (LPP) was tested on day 7 after VD; Nrf2 expression, apoptosis, and MDA levels were then measured in urethra and anterior vaginal wall. Mechanical stretch decreased Nrf2 messenger RNA (mRNA) and protein expressions. Overexpression of Nrf2 alleviated mechanical-stretch-induced cell apoptosis; S-phase arrest of cell cycle; up-regulation of Bax, cytochrome C (Cyt-C), ROS, MDA, ratio of cleaved-caspase-3/caspase-3 and cleaved-caspase-9/caspase-9; and exacerbated the decrease of Bcl2 and ΔΨm in L929 cells. On the contrary, silencing of Nrf2 showed opposite effects. Besides, VD reduced LPP levels and Nrf2 expression and increased cell apoptosis and MDA generation in the urethra and anterior vaginal wall. Nrf2 exhibits a protective role against mechanical-stretch -induced apoptosis on mouse fibroblasts, which might indicate a potential therapeutic target of mechanical-trauma-induced stress urinary incontinence (SUI).

Mechanical system design in the engineering design of digital x-ray

International Nuclear Information System (INIS)

Muhammad Awwaluddin; I Putu Susila; Edy Purwanta; Abdul Jalil; Ahmad H

2014-01-01

Has been designed a mechanical system design to hold and moving the x-ray tube, detector films, and a place the holder control box. The design was conducted on the frame foundation, frame columns and frame arms in order to operate the device as well SS304 hollow measuring 40 x 60 x mm with thickness of 2 mm long 4.1 m, size 100 x 100 mm and 2 mm thick along the 2 m, and the size of 40 x 80 mm thickness 2 mm long 1.8 m is needed to reactive the design the linear guide way models HGW20HB 3 m. With the proposed design, the operation of the digital x-rays can be completed as well. (author)

Photodissociation dynamics of CH3C(O)SH in argon matrix: A QM/MM nonadiabatic dynamics simulation

Science.gov (United States)

Xia, Shu-Hua; Liu, Xiang-Yang; Fang, Qiu; Cui, Ganglong

2015-11-01

In this work, we have first employed the combined quantum mechanics/molecular mechanics (QM/MM) method to study the photodissociation mechanism of thioacetic acid CH3C(O)SH in the S1, T1, and S0 states in argon matrix. CH3C(O)SH is treated quantum mechanically using the complete active space self-consistent field and complete active space second-order perturbation theory methods; argon matrix is described classically using Lennard-Jones potentials. We find that the C-S bond fission is predominant due to its small barriers of ca. 3.0 and 1.0 kcal/mol in the S1 and T1 states. It completely suppresses the nearby C—C bond fission. After the bond fission, the S1 radical pair of CH3CO and SH can decay to the S0 and T1 states via internal conversion and intersystem crossing, respectively. In the S0 state, the radical pair can either recombine to form CH3C(O)SH or proceed to form molecular products of CH2CO and H2S. We have further employed our recently developed QM/MM generalized trajectory-based surface-hopping method to simulate the photodissociation dynamics of CH3C(O)SH. In 1 ps dynamics simulation, 56% trajectories stay at the Franck-Condon region; the S1 C—S bond fission takes place in the remaining 44% trajectories. Among all nonadiabatic transitions, the S1 → S0 internal conversion is major (55%) but the S1 → T1 intersystem crossing is still comparable and cannot be ignored, which accounts for 28%. Finally, we have found a radical channel generating the molecular products of CH2CO and H2S, which is complementary to the concerted molecular channel. The present work sets the stage for simulating photodissociation dynamics of similar thio-carbonyl systems in matrix.

Physico-chemical mechanism for the vapors sensitivity of photoluminescent InP quantum dots

Science.gov (United States)

Prosposito, P.; De Angelis, R.; De Matteis, F.; Hatami, F.; Masselink, W. T.; Zhang, H.; Casalboni, M.

2016-03-01

InP/InGaP surface quantum dots are interesting materials for optical chemical sensors since they present an intense emission at room temperature, whose intensity changes rapidly and reversibly depending on the composition of the environmental atmosphere. We present here their emission properties by time resolved photoluminescence spectroscopy investigation and we discuss the physico-chemical mechanism behind their sensitivity to the surrounding atmosphere. Photoluminescence transients in inert atmosphere (N2) and in solvent vapours of methanol, clorophorm, acetone and water were measured. The presence of vapors of clorophorm, acetone and water showed a very weak effect on the transient times, while an increase of up to 15% of the decay time was observed for methanol vapour exposure. On the basis of the vapor molecule nature (polarity, proticity, steric hindrance, etc.) and of the interaction of the vapor molecules with the quantum dots surface a sensing mechanism involving quantum dots non-radiative surface states is proposed.

Physico-chemical mechanism for the vapors sensitivity of photoluminescent InP quantum dots

International Nuclear Information System (INIS)

Prosposito, P.; De Angelis, R.; De Matteis, F.; Casalboni, M.; Hatami, F.; Masselink, W.T.; Zhang, H.

2016-01-01

InP/InGaP surface quantum dots are interesting materials for optical chemical sensors since they present an intense emission at room temperature, whose intensity changes rapidly and reversibly depending on the composition of the environmental atmosphere. We present here their emission properties by time resolved photoluminescence spectroscopy investigation and we discuss the physico-chemical mechanism behind their sensitivity to the surrounding atmosphere. Photoluminescence transients in inert atmosphere (N 2 ) and in solvent vapours of methanol, chloroform, acetone and water were measured. The presence of vapors of chloroform, acetone and water showed a very weak effect on the transient times, while an increase of up to 15% of the decay time was observed for methanol vapour exposure. On the basis of the vapor molecule nature (polarity, proticity, steric hindrance, etc.) and of the interaction of the vapor molecules with the quantum dots surface a sensing mechanism involving quantum dots non-radiative surface states is proposed. (paper)

A comparison of treatment modalities for renal calculi between 100 and 300 mm2: are shockwave lithotripsy, ureteroscopy, and percutaneous nephrolithotomy equivalent?

Science.gov (United States)

Wiesenthal, Joshua D; Ghiculete, Daniela; D'A Honey, R John; Pace, Kenneth T

2011-03-01

Shockwave lithotripsy (SWL) is considered a standard treatment for patients with upper-tract stones that are less than 10 mm in diameter, whereas stones that are larger than 20 mm are best managed by percutaneous nephrolithotomy (PCNL). The management of stones between these sizes remains controversial. Our purpose was to review our contemporary series of SWL, ureteroscopy (URS), and PCNL outcomes for intermediate-sized upper tract calculi (100-300 mm(2)). Analysis was restricted to those patients who were treated for a renal calculus that measured between 100 and 300 mm(2) during a 4-year span. Demographic, stone, patient, treatment, and follow-up data were collected from a prospectively maintained database. A total of 137 patients were referred with nonstaghorn calculi with an area between 100 and 300 mm(2). Fifty-three (38.7%) patients were treated with SWL, while 41 (29.9%) and 43 (31.4%) underwent ureteroscopy and PCNL, respectively. Mean stone area was higher in the PCNL group (P < 0.001), whereas stone density was higher for patients undergoing SWL (P = 0.002). Single treatment success rates were better for PCNL at 95.3%,vs 87.8% for ureteroscopy and 60.4% for SWL, P < 0.001. When allowing for two SWL treatments, the success rate improved to 79.2%, thus equalizing the success of the three treatment modalities (P = 0.66). Auxiliary treatments were more common after SWL (42.3%; P < 0.01). For intermediate-sized upper-tract stones, when allowing for up to two SWL treatments, there was no significant difference between treatment modalities. Thus, SWL is a reasonably successful treatment alternative for patients who are not fit for a general anesthetic or who prefer SWL over competing treatments, provided they accept a potentially higher number of treatments.

Diagnosis of aggressive subtypes of eyelid basal cell carcinoma by 2-mm punch biopsy: prospective and comparative study.

Science.gov (United States)

Rossato, Luiz Angelo; Carneiro, Rachel Camargo; Macedo, Erick Marcet Santiago de; Lima, Patrícia Picciarelli de; Miyazaki, Ahlys Ayumi; Matayoshi, Suzana

2016-01-01

: to compare the accuracy of preoperative 2-mm punch biopsy at one site and at two sites in the diagnosis of aggressive subtypes of eyelid basal cell carcinoma (BCC). : we randomly assigned patients to Group 1 (biopsy at one site) and Group 2 (biopsy at two sites). We compared the biopsy results to the gold standard (pathology of the surgical specimen). We calculated the sensitivity, specificity, positive predictive value, negative predictive value, accuracy and Kappa coefficient to determine the level of agreement in both groups. : we analyzed 105 lesions (Group 1: n = 44; Group 2: n = 61). The agreement was 54.5% in Group 1 and 73.8% in Group 2 (p = 0.041). There was no significant difference between the groups regarding the distribution of quantitative and qualitative variables (gender, age, disease duration, tumor larger diameter, area and commitment of margins). Biopsy at two sites was two times more likely to agree with the gold standard than the biopsy of a single site. : the accuracy and the performance indicators were better for 2-mm punch biopsy in two sites than in one site for the diagnosis of aggressive subtypes of eyelid BCC. comparar a acurácia da biópsia pré-operatória por trépano de 2mm em um sítio e em dois sítios no diagnóstico dos subtipos agressivos de carcinoma basocelular (CBC) palpebral. os pacientes foram distribuídos aleatoriamente em Grupo 1 (biópsia em um sítio) e Grupo 2 (biópsia em dois sítios). Os resultados das biópsias foram comparados com o padrão-ouro (exame anatomopatológico da peça cirúrgica). A sensibilidade, especificidade, valor preditivo positivo, valor preditivo negativo, precisão e coeficiente Kappa foram calculados para determinar o nível de concordância nos dois grupos. foram analisadas 105 lesões (Grupo 1: n = 44; Grupo 2: n = 61). A concordância foi de 54,5% no Grupo 1 e 73,8% no Grupo 2 (p-valor = 0,041). Não houve diferença significativa entre os grupos quanto à distribuição das vari

Image Quality Assessment of 2D versus 3D T2WI and Evaluation of Ultra-high b-Value (b=2,000 mm/s2) DWI for Response Assessment in Rectal Cancer.

Science.gov (United States)

Hausmann, Daniel; Liu, Jing; Budjan, Johannes; Reichert, Miriam; Ong, Melissa; Meyer, Mathias; Smakic, Arman; Grimm, Robert; Strecker, Ralph; Schoenberg, Stefan O; Wang, Xiaoying; Attenberger, Ulrike I

2018-02-01

The purpose of this IRB-approved, retrospective study was to compare image quality between 2D and high-resolution 3D, T2-weighted (T2WI) magnetic resonance imaging (MRI) sequences and to investigate the additional value of ultra-high b-value diffusion-weighted imaging (DWI; b=2,000 mm/s 2 ) for both rectal cancer staging and evaluating treatment response. From 12 February to 24 August 2016, 26 consecutive patients (22 males, four females; mean age: 61.9±14.0 years) with histologically-proven rectal cancer. In total 31 examinations [12 prior to and 19 after chemoradiation (CRT)] were included. The patients underwent pelvic MRI on a 3.0-T scanner (Magnetom Skyra, Erlangen, Germany). Three radiologists (3, 4, and 5 years of experience in MRI, respectively) independently assessed all images and rated the image quality of DWI (b=800 mm/s 2 ), apparent diffusion coefficient map, DWI (b=2,000 mm/s 2 ), 3D sagittal T2WI, 3D axial T2WI, 2D sagittal T2WI, and 2D axial T2WI of each patient, respectively. In addition, signal intensity ratios (SIR) were calculated between rectal cancer and obturator internus muscle (background) in all patients after CRT on DWI (b=2,000 mm/s 2 ) and correlated with histopathological regression grade (RG). Tumor delineation was significantly better by 2D T2WI than 3D T2WI both before and after CRT (before CRT: Z=-3.2, p=0.02; after CRT: Z=-4.408, p3D sagittal: 4.00±0.48; 2D sagittal: 4.03±0.34, p=0.713; 3D axial: 3.85±0.61, 2D axial: 3.78±0.64, p=0.537). Independent t-test showed significantly higher SIR between those with RG 1 or 2 (moderate response: mean score=2.02) and those with RG 3+4 (good response: mean score=0.8) (t=3.044, p=0.011). In those with RG 4 (complete response), SIR of b2000 was 0.946 compared to a 1.41 average of the whole cohort. In two patients, tumor was invisible on b2000 following CRT (RG 3 and 4, respectively). Interobserver agreement was mostly good (κ≥0.6) regarding image quality assessment, except for poor

Study of the Artroscopic Anatomy of the Knee in Canine Cadavers Using 2.4 Mm Diameter Lens

Directory of Open Access Journals (Sweden)

Gabriel Oswaldo Alonso Cuéllar

2013-05-01

Full Text Available Mainly by a limited access to new techniques and technologies, veterinary medicine in developing countries, has been far behind from the human medicine. One of the causes is the limited access to technology and specific techniques. Moreover, it is clear that many new technologies have proven their benefits in the two disciplines, making necessary and almost mandatory their massive implementation in humans and animals. The possibility to use human elements for veterinary techniques would improve the technology access and veterinarians training, at lower costs. The purpose of this study is to verify the feasibility to perform a knee arthroscopy in dogs with small human joints arthroscopic lenses. Under protocols established in veterinary 12 knee arthroscopies were performed in canine cadaver, using a wrist and ankle arthroscope human of 2.4 mm in diameter and 30° of angulation. All the structures reported in the literature were possible to visualize using a 2.4 mm arthroscope. In this sense, it is possible to develop training activities and subsequent implementation of endoscopic techniques in canine femorotibiopatellar joint, using a lens of small joints of human medicine.

Steric Interference of Adhesion Supports In-Vitro Chondrogenesis of Mesenchymal Stem Cells on Hydrogels for Cartilage Repair.

Science.gov (United States)

Goldshmid, Revital; Cohen, Shlomit; Shachaf, Yonatan; Kupershmit, Ilana; Sarig-Nadir, Offra; Seliktar, Dror; Wechsler, Roni

2015-09-28

Recent studies suggest the presence of cell adhesion motifs found in structural proteins can inhibit chondrogenesis. In this context, the current study aims to determine if a polyethylene glycol (PEG)-modified fibrinogen matrix could support better chondrogenesis of human bone marrow mesenchymal stem cells (BM-MSC) based on steric interference of adhesion, when compared to a natural fibrin matrix. Hydrogels used as substrates for two-dimensional (2D) BM-MSC cultures under chondrogenic conditions were made from cross-linked PEG-fibrinogen (PF) and compared to thrombin-activated fibrin. Cell morphology, protein expression, DNA and sulfated proteoglycan (GAG) content were correlated to substrate properties such as stiffness and adhesiveness. Cell aggregation and chondrogenic markers, including collagen II and aggrecan, were observed on all PF substrates but not on fibrin. Shielding fibrinogen's adhesion domains and increasing stiffness of the material are likely contributing factors that cause the BM-MSCs to display a more chondrogenic phenotype. One composition of PF corresponding to GelrinC™--a product cleared in the EU for cartilage repair--was found to be optimal for supporting chondrogenic differentiation of BM-MSC while minimizing hypertrophy (collagen X). These findings suggest that semi-synthetic biomaterials based on ECM proteins can be designed to favourably affect BM-MSC towards repair processes involving chondrogenesis.

SUBMILLIMETER ARRAY OBSERVATIONS TOWARD THE MASSIVE STAR-FORMING CORE MM1 OF W75N

International Nuclear Information System (INIS)

Minh, Y. C.; Su, Y.-N.; Liu, S.-Y.; Yan, C.-H.; Chen, H.-R.; Kim, S.-J.

2010-01-01

The massive star-forming core MM1 of W75N was observed using the Submillimeter Array with ∼1'' and 2'' spatial resolutions at 217 and 347 GHz, respectively. From the 217 GHz continuum we found that the MM1 core consists of two sources, separated by about 1'': MM1a (∼0.6 M sun ) and MM1b (∼1.4 M sun ), located near the radio continuum sources VLA 2/VLA 3 and VLA 1, respectively. Within MM1b, two gas clumps were found to be expanding away from VLA 1 at about ±3 km s -1 , as a result of the most recent star formation activity in the region. Observed molecular lines show emission peaks at two positions, MM1a and MM1b: sulfur-bearing species have emission peaks toward MM1a, but methanol and saturated species at MM1b. We identified high-temperature (∼200 K) gas toward MM1a and the hot core in MM1b. This segregation may result from the evolution of the massive star-forming core. In the very early phase of star formation, the hot core is seen through the evaporation of dust ice-mantle species. As the mantle species are consumed via evaporation the high-temperature gas species (such as the sulfur-bearing molecules) become bright. The SiO molecule is unique in having an emission peak exactly at the VLA 2 position, probably tracing a shock powered by VLA 2. The observed sulfur-bearing species show similar abundances both in MM1a and MM1b, whereas the methanol and saturated species show significant abundance enhancement toward MM1b, by about an order of magnitude, compared to MM1a.

A self-consistent MoD-WM/MM structural refinement method: characterization of hydrogen bonding in the orytricha nova G-1uar

Energy Technology Data Exchange (ETDEWEB)

Batista, Enrique R [Los Alamos National Laboratory; Newcomer, Micharel B [YALE UNIV; Raggin, Christina M [YALE UNIV; Gascon, Jose A [YALE UNIV; Loria, J Patrick [YALE UNIV; Batista, Victor S [YALE UNIV

2008-01-01

This paper generalizes the MoD-QM/MM hybrid method, developed for ab initio computations of protein electrostatic potentials [Gasc6n, l.A.; Leung, S.S.F.; Batista, E.R.; Batista, V.S. J. Chem. Theory Comput. 2006,2, 175-186], as a practical algorithm for structural refinement of extended systems. The computational protocol involves a space-domain decomposition scheme for the formal fragmentation of extended systems into smaller, partially overlapping, molecular domains and the iterative self-consistent energy minimization of the constituent domains by relaxation of their geometry and electronic structure. The method accounts for mutual polarization of the molecular domains, modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) environment according to QM/MM hybrid methods. The method is applied to the description of benchmark models systems that allow for direct comparisons with full QM calculations, and subsequently applied to the structural characterization of the DNA Oxytricha nova Guanine quadruplex (G4). The resulting MoD-QM/MM structural model of the DNA G4 is compared to recently reported highresolution X-ray diffraction and NMR models, and partially validated by direct comparisons between {sup 1}H NMR chemical shifts that are highly sensitive to hydrogen-bonding and stacking interactions and the corresponding theoretical values obtained at the density functional theory DFT QM/MM (BH&H/6-31 G*:Amber) level in conjunction with the gauge independent atomic orbital (GIAO) method for the ab initio self consistent-field (SCF) calculation of NMR chemical shifts.

Quantum and Statistical Mechanics Applied to Singlet Carbenes, Pericyclic Reactions, and Condensed Phase Phenomena

Science.gov (United States)

Evanseck, Jeffrey Donald

The completed research covers a broad range of theoretical applications in organic chemistry. It is divided into three chapters which covers the chemistry of singlet carbenes (Chapter 1), substituent effects in pericyclic rearrangements (Chapter 2), and the effects of solvent on the reactivity of organic reactions (Chapter 3). The selectivity between 1,2- and 1,4-intramolecular additions to restricted diene systems has been investigated. A decrease in activation energy for the intramolecular cycloaddition is noted for systems which approach the idealized geometry found with intermolecular addition of carbenes to olefins. Direct substitution at the carbene site dramatically effects the predicted activation barriers for 1,2-hydrogen shifts. An excellent correlation between the activation energy and a substituents sigma_sp {rm R}{rm o} parameters has been demonstrated. The long standing problem of orbital alignment influences on the selectivity of 1,2-hydrogen arrangements shows significant geometric distortions, yet has little influence on the rates of singlet alkylcarbene rearrangements. The exo-selectivities observed for 1,2-shifts in rigid systems are explained by torsional and steric interactions which develop in the transition structures. Substituent effects on pericyclic reactions have been computed for several conrotatory and disrotatory electrocyclizations. The six-electron disrotatory electrocyclization of 1-substituted hexatrienes displays a strong electronic component in determining stereoselectivity, despite incredible steric interference. The eight-electron conrotatory electrocyclization transition structure of 1-substituted octatetraene has an unusual helical transition structure which does not differentiate between substituent position. The effects of solvents on the acidity differences between E and Z esters has supplemented earlier ab initio quantum mechanical results on the enhanced acidity of Meldrum's acid. Monte Carlo simulations predict a

A ±6 ms-Accuracy, 0.68 mm2, and 2.21 μW QRS Detection ASIC

Directory of Open Access Journals (Sweden)

Sheng-Chieh Huang

2012-01-01

Full Text Available Healthcare issues arose from population aging. Meanwhile, electrocardiogram (ECG is a powerful measurement tool. The first step of ECG is to detect QRS complexes. A state-of-the-art QRS detection algorithm was modified and implemented to an application-specific integrated circuit (ASIC. By the dedicated architecture design, the novel ASIC is proposed with 0.68 mm2 core area and 2.21 μW power consumption. It is the smallest QRS detection ASIC based on 0.18 μm technology. In addition, the sensitivity is 95.65% and the positive prediction of the ASIC is 99.36% based on the MIT/BIH arrhythmia database certification.

Diagnosis of bronchiectasis with multislice spiral CT: accuracy of 3-mm-thick structured sections

Energy Technology Data Exchange (ETDEWEB)

Remy-Jardin, Martine; Amara, Assia; Campistron, Philippe; Mastora, Ioana; Remy, Jacques [Department of Radiology, Hospital Calmette, University Center of Lille, Boulevard Jules Leclerc, 59037, Lille Cedex (France); Delannoy, Valerie; Duhamel, Alain [Department of Medical Statistics, University of Lille, Place de Verdun, 59037, Lille Cedex (France)

2003-05-01

The aim of this study was to evaluate the accuracy of 3-mm-thick reconstructed sections in the diagnosis of bronchiectasis with multislice CT (MSCT). Forty consecutive patients suspected of bronchiectasis (23 females, 17 males; mean age 51 years) underwent MSCT of the entire thorax with a 4 x 1-mm collimation (120 kV, 0.5 s/rotation, 80 mAs/slice) and a pitch of 1.75. From each data set (mean z-axis coverage: 257 mm; mean duration: 21 s), two series of images were systematically generated: 1-mm (group 1) and 3-mm (group 2)-thick reconstructed scans. Both series of images were obtained at 10-mm intervals and reconstructed with a high-spatial-frequency algorithm. Two observers independently analyzed the presence of bronchiectasis and associated abnormalities in group-1 and group-2 lung images. No significant difference between group 1 and group 2 was found in: (a) the detection of bronchiectasis, identified in 24 patients (60%) in group 1 and in 23 patients (57.5%) in group 2 (p=0.08); (b) the evaluation of the extent of bronchiectasis, identifying focal bronchiectasis in 10 patients (25%) in group 1 and 7 patients (17.5%) in group 2 (p=0.39) and multifocal bronchiectasis in 16 patients (40%) in both groups; (c) the characterisation of bronchiectasis (cylindral bronchiectasis: group 1, n=24, 60%; group 2, n=21, 53%, p=0.08); varicose bronchiectasis: group 1, n=5, 12.5%; group 2, n=6, 15%, p=0.56; and cystic bronchiectasis: group 1, n=2, 5%; group 2, n=2, 5%. Apart from the identification of abnormal bronchial wall thickening (group 2, n=35, 87.5%, vs group 1, n=31, 77.5%, p<0.05), recognition of associated bronchopulmonary anomalies did not differ between the two groups. This study demonstrates a comparable accuracy of the 3- and 1-mm-thick reconstructed scans in the detection and characterization of bronchiectasis. These results suggest the potential usefulness of 3-mm-thick scans generated from 4 x 2.5-mm acquisitions in the screening of bronchiectasis, which would

Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F- + CH3I reaction in aqueous solution.

Science.gov (United States)

Liu, Peng; Zhang, Jingxue; Wang, Dunyou

2017-06-07

A double-inversion mechanism of the F - + CH 3 I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol -1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol -1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol -1 , which agrees very well with the experimental value at 25.2 kcal mol -1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

Broadband Mm-Wave OFDM Communications in Doubly Selective Channel: Performance Evaluation Using Measured Mm-Wave Channel

DEFF Research Database (Denmark)

Chen, Xiaoming; Fan, Wei; Pedersen, Gert F.

2018-01-01

In this work, we evaluate the performance of the broadband millimeter-wave (mm-wave) OFDM system in the presence of phase noise (PN) of phase-locked loop based oscillator and delay spread of measured mm-wave channel. It is shown, using Akaike's information criterion, that the channel tap...... coefficients of the broadband mm-wave channel do not follow Gaussian distribution due to the broad bandwidth. It is also shown that, given a cyclic prefix (CP) length for a certain delay spread, an effective PN mitigation scheme enables a PN corrupted OFDM system to function with small subcarrier spacing and...

Harvest of table olives by mechanical harvesting equipment

Directory of Open Access Journals (Sweden)

Filippo Gambella

2013-09-01

Full Text Available In this work, we have evaluated the performance, of an electric comb equipped with five undulated fingers used for mechanized the harvesting of table olives. The first aim of the work was to test three different types of coating materials used for covering the fingers: Silicon (S, Vulcanized rubber (VR and Natural rubber (NR. The diameter of the coating materials tested were 7mm (D1, 14 mm (D2, 19 mm (D3 in order to evaluate the damage of different working conditions on the intact olives. During harvesting, silicon at 7mm and 14mm resulted in the largest percentage of undamaged the fruit (67% and 65%, natural rubber 63% and vulcanized rubber at the 54%. The second aim was to evaluate the combination, in terms of the best performance, of the machines used for mechanized harvesting of table olives. Several factors have been examined: undulating fingers variation thickness, different rotational speeds and different coating materials used to reduce the impact damage on olives. From the tests on olive tree we have determined that while plastic materials (S and (NR appear to have a positive role in harvest quality, the vibration transmitted to the operator’s hand is great from 6.48 m/s2 for S to 6.31 m/ s2 for NR and 2.92 m/s2 for VR, respect to the materials used.

Heat Transfer Experiments with Supercritical CO{sub 2} in a Vertical Circular Tube (9.0 mm)

Energy Technology Data Exchange (ETDEWEB)

Yoo, Tae Ho; Kim, Hwan Yeol [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Sim, Woo Gun; Bae, Yoon Yeong [Hannam University, Daejeon (Korea, Republic of)

2008-10-15

Heat transfer test facility, SPHINX(Supercritical Pressure Heat transfer Investigation for NeXt generation), has been operated at KAERI for an investigation of the thermal-hydraulic behaviors of supercritical CO{sub 2} at several test sections with a different geometry. The loop uses CO{sub 2} because it has critical pressure and temperature which is much lower than water. Experimental study of heat transfer to supercritical CO{sub 2} in a vertical circular tube with and inner diameter of 9.0mm has been performed. CO{sub 2} flows downward through the vertical circular tube for the simulation of the water rod which may be used for a moderation of the reactor. The heat transfer characteristics were analyzed and compared with the upward flow test results previously performed at the same test section at KAERI.

Phakic Intraocular Lens Implantation: Refractive Outcome and Safety in Patients with Anterior Chamber Depth between 2.8 and 3.0 versus ≥3.0 mm.

Science.gov (United States)

Guerra, Marta G; Silva, Andreia M M; Marques, Sara H M; Melo, Sofia H; Póvoa, João A; Lobo, Conceição; Murta, Joaquim Neto

2017-01-01

To compare endothelial cell (EC) variation after anterior chamber phakic intraocular lens (AC-pIOL) implantation in highly myopic patients with a preoperative anterior chamber depth (ACD) between 2.8 and 3.0 versus ≥3.0 mm. A total of 280 eyes submitted to primary AC-pIOL implantation were analyzed. Pre- and postoperative values for uncorrected distance visual acuity, corrected distance visual acuity, spherical equivalent, ACD (endothelial surface), and EC count were collected. The eyes were divided into 2 groups: group A - ACD between 2.8 and 3.0 mm; group B - ACD ≥3.0 mm. Mean global EC loss (ECL) and loss for each ACD group, according to pIOL type, were analyzed. Significant improvement of the spherical equivalent (-11.38 ± 4.57 vs. -0.49 ± 0.79; p = 0.000) and a significant decrease in EC density (2,810.95 ± 343.88 vs. 2,584.09 ± 374.88 cells/mm2; p = 0.000) were noted. The mean annual ECL was -2.19 ± 3.97%. Regarding group A (n = 80), a mean annual ECL of -2.06 ± 3.88% was registered, higher for the Acrysof Cachet® subtype, while group B (n = 200) showed -2.25 ± 4.01% ECL, higher for the Verisyse® subtype. There was no significant difference between the groups (p = 0.96). AC-pIOL implantation significantly improves the spherical equivalent in myopic patients. The mean annual ECL after pIOL implantation was higher in the larger ACD group, but this value was not statistically significant. A 2.8-mm ACD value seems to be a safe cutoff for AC-pIOL implantation. © 2017 S. Karger AG, Basel.

Photodissociation dynamics of CH{sub 3}C(O)SH in argon matrix: A QM/MM nonadiabatic dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Xia, Shu-Hua; Liu, Xiang-Yang; Fang, Qiu; Cui, Ganglong, E-mail: ganglong.cui@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)

2015-11-21

In this work, we have first employed the combined quantum mechanics/molecular mechanics (QM/MM) method to study the photodissociation mechanism of thioacetic acid CH{sub 3}C(O)SH in the S{sub 1}, T{sub 1}, and S{sub 0} states in argon matrix. CH{sub 3}C(O)SH is treated quantum mechanically using the complete active space self-consistent field and complete active space second-order perturbation theory methods; argon matrix is described classically using Lennard-Jones potentials. We find that the C-S bond fission is predominant due to its small barriers of ca. 3.0 and 1.0 kcal/mol in the S{sub 1} and T{sub 1} states. It completely suppresses the nearby C—C bond fission. After the bond fission, the S{sub 1} radical pair of CH{sub 3}CO and SH can decay to the S{sub 0} and T{sub 1} states via internal conversion and intersystem crossing, respectively. In the S{sub 0} state, the radical pair can either recombine to form CH{sub 3}C(O)SH or proceed to form molecular products of CH{sub 2}CO and H{sub 2}S. We have further employed our recently developed QM/MM generalized trajectory-based surface-hopping method to simulate the photodissociation dynamics of CH{sub 3}C(O)SH. In 1 ps dynamics simulation, 56% trajectories stay at the Franck-Condon region; the S{sub 1} C—S bond fission takes place in the remaining 44% trajectories. Among all nonadiabatic transitions, the S{sub 1} → S{sub 0} internal conversion is major (55%) but the S{sub 1} → T{sub 1} intersystem crossing is still comparable and cannot be ignored, which accounts for 28%. Finally, we have found a radical channel generating the molecular products of CH{sub 2}CO and H{sub 2}S, which is complementary to the concerted molecular channel. The present work sets the stage for simulating photodissociation dynamics of similar thio-carbonyl systems in matrix.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

Science.gov (United States)

Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

2015-01-01

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

Effect of physical and mechanical properties of cassava tubers on the performance of an automated peeling machine

Directory of Open Access Journals (Sweden)

O.C. Ademosun

2012-12-01

Full Text Available Peeling of cassava tuber at all levels is still largely carried out manually; however, this work is presented with a view to investigate the effect of physical and mechanical properties of cassava tubers on mechanical peeling and hence provides a basis for cassava peeling mechanization. These properties include size of the tuber, tl, proportion by weight of peel, wp, average moisture content of the peel, map, peel thickness, tp, tuber diameter, td, tuber surface taper angle, α, peel penetration force, F, and peel shearing stress, ts. The results showed that for Slmhf; tl ranged from 140-460mm, wp ranged from 13.12-20.06%, map was 76.27%, tp ranged from 1.62-4.34mm, td ranged from 31.08-136.63mm, α ranged from 9.03-23.130, F ranged from 0.17-1.85N/mm, ts ranged from 0.85-9.25N/mm2 and quality performance of the machine, QPE, for this tuber ranged from 70.82-96.21%. Similarly, for Ssmlf; tl ranged from 125-362mm, wp ranged from 10.52-16.66%, map was 70.97%, tp ranged from 1.22-4.12mm, td ranged from 18.86-99.29mm, α ranged from 5.20-12.290, F ranged from 0.13-1.54N/mm, ts ranged from 0.65-7.70N/mm2 and quality performance of the machine, QPE, for this tuber ranged from 67.27-92.25 %. The results confirm influence of physico-mechanical properties of cassava tuber on mechanical peeling.

Ester versus polyketone formation in the palladium-diphosphine catalyzed carbonylation of ethene.

Science.gov (United States)

Zuidema, Erik; Bo, Carles; van Leeuwen, Piet W N M

2007-04-04

The origin of the chemoselectivity of palladium catalysts containing bidentate phosphine ligands toward either methoxycarbonylation of ethene or the copolymerization of ethene and carbon monoxide was investigated using density functional theory based calculations. For a palladium catalyst containing the electron-donating bis(dimethylphosphino)ethane (dmpe) ligand, the rate determining step for chain propagation is shown to be the insertion of ethene into the metal-acyl bond. The high barrier for chain propagation is attributed to the low stability of the ethene intermediate, (dmpe)Pd(ethene)(C(O)CH3). For the competing methanolysis process, the most likely pathway involves the formation of (dmpe)Pd(CH3OH)(C(O)CH3) via dissociative ligand exchange, followed by a solvent mediated proton-transfer/reductive- elimination process. The overall barrier for this process is higher than the barrier for ethene insertion into the palladium-acetyl bond, in line with the experimentally observed preference of this type of catalyst toward the formation of polyketone. Electronic bite angle effects on the rates of ethene insertion and ethanoyl methanolysis were evaluated using four electronically and sterically related ligands (Me)2P(CH2)nP(Me)2 (n = 1-4). Steric effects were studied for larger tert-butyl substituted ligands using a QM/MM methodology. The results show that ethene coordination to the metal center and subsequent insertion into the palladium-ethanoyl bond are disfavored by the addition of steric bulk around the metal center. Key intermediates in the methanolysis mechanism, on the other hand, are stabilized because of electronic effects caused by increasing the bite angle of the diphosphine ligand. The combined effects explain successfully which ligands give polymer and which ones give methyl propionate as the major products of the reaction.

The isotypic family of the diarsenates MM'As{sub 2}O{sub 7} (M = Sr, Ba; M' = Cd, Hg)

Energy Technology Data Exchange (ETDEWEB)

Weil, Matthias [Technische Univ. Wien (Austria). Inst. for Chemical Technologies and Analytics

2016-08-01

The diarsenates MM'As{sub 2}O{sub 7} (M = Sr, Ba; M' = Cd, Hg) were prepared under hydrothermal conditions (∝200 C, autogenous pressure), starting from As{sub 2}O{sub 5} and the corresponding metal oxides or precursor compounds thereof in aqueous solutions. Structure analyses on the basis of single crystal X-ray data revealed the four structures to be isotypic. They are the first diarsenates to crystallize in the triclinic BaZnP{sub 2}O{sub 7} structure type (space group P anti 1, Z = 2, a ∼ 5.8 Aa, b ∼ 7.3 Aa, c ∼ 7.6 Aa, α ∼ 101 , β ∼ 91 , γ ∼ 98 ). All related MM'As{sub 2}O{sub 7} diarsenates reported so far (M = Sr, Ba, Pb; M' = Mg, Co, Cu, Zn) crystallize in the monoclinic α-Ca{sub 2}P{sub 2}O{sub 7} structure type (P2{sub 1}/n, Z = 4). Hence, the size of the divalent M' cation determines which of the two structure types is adopted.

Accelerator Quality HTS Dipole Magnet Demonstrator designs for the EuCARD-2, 5 Tesla 40 mm Clear Aperture Magnet

CERN Document Server

Kirby, G; Ballarino, A; Bottura, L; Chouika, N; Clement, S; Datskov, V; Fajardo, L; Fleiter, J; Gauthier, R; Lambert, L; Lopes, M; Perez, J; DeRijk, G; Rijllart, A; Rossi, L; Ten Kate, H; Durante, M; Fazilleau, P; Lorin, C; Haro, E; Stenvall, A; Caspi, S; Marchevsky, M; Goldacker, W; Kario, A

2014-01-01

Future high-energy accelerators will need very high magnetic fields in the range of 20 T. The EuCARD-2 work-package-10 is a collaborative push to take HTS materials into an accelerator quality demonstrator magnet. The demonstrator will produce 5 T standalone and between 17 T and 20 T, when inserted into the 100 mm aperture of Fresca-2 high field out-sert magnet. The HTS magnet will demonstrate the field strength and field quality that can be achieved. An effective quench detection and protection system will have to be developed to operate with the HTS superconducting materials. This paper presents a ReBCO magnet design using multi strand Roebel cable that develops a stand-alone field of 5 T in a 40 mm clear aperture and discusses the challenges associated with good field quality using this type of material. A selection of magnet designs is presented as result of a first phase of development.

Accelerator Quality HTS Dipole Magnet Demonstrator Designs for the EuCARD-2, 5 Tesla 40 mm Clear Aperture Magnet

CERN Document Server

Kirby, G A; Ballarino, A; Bottura, L; Chouika, N; Clement, S; Datskov, V; Fajardo, L; Fleiter, J; Gauthier, R; Gentini, L; Lambert, L; Lopes, M; Perez, J C; de Rijk, G; Rijllart, A; Rossi, L; ten Kate, H; Durante, M; Fazilleau, P; Lorin, C; Härö, E; Stenvall, A; Caspi, S; Marchevsky, M; Goldacker, W; Kario, A

2015-01-01

Future high-energy accelerators will need very high magnetic fields in the range of 20 T. The EuCARD-2 work-package-10 is a collaborative push to take HTS materials into an accelerator quality demonstrator magnet. The demonstrator will produce 5 T standalone and between 17 T and 20 T, when inserted into the 100 mm aperture of Fresca-2 high field out-sert magnet. The HTS magnet will demonstrate the field strength and field quality that can be achieved. An effective quench detection and protection system will have to be developed to operate with the HTS superconducting materials. This paper presents a ReBCO magnet design using multi strand Roebel cable that develops a stand-alone field of 5 T in a 40 mm clear aperture and discusses the challenges associated with good field quality using this type of material. A selection of magnet designs is presented as result of a first phase of development.

Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation.

Science.gov (United States)

Dutta, Debodyuti; Mishra, Sabyashachi

2017-07-27

The mechanism of the catalytic hydrolysis of N-succinyl diaminopimelic acid (SDAP) by the microbial enzyme DapE in its wild-type (wt) form as well as three of its mutants (E134D, H67A, and H349A) is investigated employing a hybrid quantum mechanics/molecular mechanics (QM/MM) method coupled with molecular dynamics (MD) simulations, wherein the time evolution of the atoms of the QM and MM regions are obtained from the forces acting on the individual atoms. The free-energy profiles along the reaction coordinates of this multistep hydrolysis reaction process are explored using a combination of equilibrium and nonequilibrium (umbrella sampling) QM/MM-MD simulation techniques. In the enzyme-substrate complexes of wt-DapE and the E134D mutant, nucleophilic attack is found to be the rate-determining step involving a barrier of 15.3 and 21.5 kcal/mol, respectively, which satisfactorily explains the free energy of activation obtained from kinetic experiments in wt-DapE-SDAP (15.2 kcal/mol) and the 3 orders of magnitude decrease in the catalytic activity due to E134D mutation. The catalysis is found to be quenched in the H67A and H349A mutants of DapE due to conformational rearrangement in the active site induced by the absence of the active site His residues that prohibits activation of the catalytic water molecule.

Observations on dual-ended readout of 100 mm long LYSO crystals

Energy Technology Data Exchange (ETDEWEB)

Ur-Rehman, Fazal, E-mail: Fazal@physics.umanitoba.ca [Department of Physics and Astronomy, University of Manitoba, Winnipeg (Canada); McIntosh, Bryan [Department of Physics and Astronomy, University of Manitoba, Winnipeg (Canada); Goertzen, Andrew L. [Department of Physics and Astronomy, University of Manitoba, Winnipeg (Canada); Department of Radiology, University of Manitoba, Winnipeg (Canada)

2011-10-01

We are investigating using dual-ended readout of axially oriented long thin scintillator crystals in detectors for a compact geometry, small ring diameter animal PET system. The axial position of interaction is determined from the light sharing between two photodetectors at opposite ends of the crystal. We examine the light output, energy resolution and axial spatial resolution of 1.5-5x2x100 mm{sup 3} polished LYSO crystals by irradiating with an electronically collimated beam of 511 keV photons oriented perpendicular to the long axis and read out at either end by position sensitive photomultiplier tubes (PSPMTs). Three reflector materials, namely Teflon, 3 M enhanced specular reflector (ESR) and black paint are examined for the 2x2x100 mm{sup 3} crystal size. The light output increases and energy resolution improves with the crystal cross-section. Generally, the spatial resolution worsens with increase in crystal cross-section. For the 2x2x100 mm{sup 3} crystal size, the mean energy resolutions of the photopeak over the nine irradiation positions were 14.4{+-}0.4%, 16.0{+-}1.2% and 28.3{+-}2.1% with mean spatial resolutions of 7.0{+-}1.0, 9.4{+-}3.3 and 26.0{+-}5.0 mm using ESR, Teflon and black paint, respectively. ESR reflector gave the best light output, energy and axial spatial resolutions. These characterization results of PSPMT-based dual-ended long LYSO crystals will be useful in the design of detector modules for a highly compact geometry preclinical PET system using this detector technology.

Piezo proteins are pore-forming subunits of mechanically activated channels.

Science.gov (United States)

Coste, Bertrand; Xiao, Bailong; Santos, Jose S; Syeda, Ruhma; Grandl, Jörg; Spencer, Kathryn S; Kim, Sung Eun; Schmidt, Manuela; Mathur, Jayanti; Dubin, Adrienne E; Montal, Mauricio; Patapoutian, Ardem

2012-02-19

Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) induce mechanically activated cationic currents in cells; however, it is unknown whether Piezo proteins are pore-forming ion channels or modulate ion channels. Here we show that Drosophila melanogaster Piezo (DmPiezo, also called CG8486) also induces mechanically activated currents in cells, but through channels with remarkably distinct pore properties including sensitivity to the pore blocker ruthenium red and single channel conductances. MmPiezo1 assembles as a ∼1.2-million-dalton homo-oligomer, with no evidence of other proteins in this complex. Purified MmPiezo1 reconstituted into asymmetric lipid bilayers and liposomes forms ruthenium-red-sensitive ion channels. These data demonstrate that Piezo proteins are an evolutionarily conserved ion channel family involved in mechanotransduction.

Broadband Mm-Wave OFDM Communications in Doubly Selective Channel: Performance Evaluation Using Measured Mm-Wave Channel

DEFF Research Database (Denmark)

Chen, Xiaoming; Fan, Wei; Pedersen, Gert F.

2018-01-01

coefficients of the broadband mm-wave channel do not follow Gaussian distribution due to the broad bandwidth. It is also shown that, given a cyclic prefix (CP) length for a certain delay spread, an effective PN mitigation scheme enables a PN corrupted OFDM system to function with small subcarrier spacing and......In this work, we evaluate the performance of the broadband millimeter-wave (mm-wave) OFDM system in the presence of phase noise (PN) of phase-locked loop based oscillator and delay spread of measured mm-wave channel. It is shown, using Akaike's information criterion, that the channel tap......, therefore, small CP overhead, with only slight degradation of the error rate performance....

FT-Raman and QM/MM study of the interaction between histamine and DNA

International Nuclear Information System (INIS)

Ruiz-Chica, A.J.; Soriano, A.; Tunon, I.; Sanchez-Jimenez, F.M.; Silla, E.; Ramirez, F.J.

2006-01-01

The interaction between histamine and highly polymerized calf-thymus DNA has been investigated using FT-Raman spectroscopy and the hybrid QM/MM (quantum mechanics/molecular mechanics) methodology. Raman spectra of solutions containing histamine and calf-thymus DNA, at different molar ratios, were recorded. Solutions were prepared at physiological settings of pH and ionic strength, using both natural and heavy water as the solvent. The analysis of the spectral changes on the DNA Raman spectra when adding different concentrations of histamine allowed us to identify the reactive sites of DNA and histamine, which were used to built two minor groove and one intercalated binding models. They were further used as starting points of the QM/MM theoretical study. However, minimal energy points were only reached for the two minor groove models. For each optimized structure, we calculated analytical force constants of histamine molecule in order to perform the vibrational dynamics. Normal mode descriptions allowed us to compare calculated wavenumbers for DNA-interacting histamine to those measured in the Raman spectra of DNA-histamine solutions

Study of the degradation mechanisms of amines used for the capture of CO{sub 2} in industrial fumes; Etude des mecanismes de degradation des amines utilisees pour le captage du CO{sub 2} dans les fumees

Energy Technology Data Exchange (ETDEWEB)

Lepaumier, H

2008-10-15

Global warming leads to reduce greenhouse gas emissions. Post combustion CO{sub 2} capture with solvent is the most advanced technology to reduce CO{sub 2} emissions in industrial fumes. A major problem associated with chemical absorption of CO{sub 2} using the benchmark ethanolamine (MEA) is solvent degradation through irreversible side reactions with CO{sub 2} and O{sub 2} which leads to numerous harmful impacts to the process: corrosion, solvent loss, foaming, fouling, and viscosity increase. So, developing new amines with higher chemical stability is essential. This work is based on the chemical stability study of 17 different molecules. Their structures have been chosen in order to establish structure-property relationships: alkanolamines, known for gas treatment application (MEA, DEA, MDEA, AMP...), di-amines, and tri-amines without alcohol function. Impact of temperature, CO{sub 2}, and O{sub 2} on degradation has been studied. Strong experimental conditions have been used to observe significant degradation after a 15 days experiment. Separation, identification and quantification of degradation products have been performed by using different testing instructions such as gas chromatography, mass spectrometry, ionic chromatography and NMR. Different mechanisms are proposed to explain most of degradation compounds. Radical reactions (dealkylation, alkylation, ring-closure reactions and piperazinones formation) are involved under O{sub 2} pressure whereas CO{sub 2} induces ionic reactions (dealkylation, alkylation, addition, ring-closure reactions and oxazolidinones or imidazolidinones formation). Large discrepancies of stability are noticed among the different amines. Knowledge of degradation products and reaction mechanisms has thus permitted to establish some relationships between structure and chemical stability: for example, role of the amine function (primary, secondary, tertiary), impact of alkyl chain length between the two amino groups and steric

Mechanical evaluation of space closure loops in Orthodontics

OpenAIRE

Rodrigues, Eduardo Uggeri; Maruo, Hiroshi; Guariza Filho, Odilon; Tanaka, Orlando; Camargo, Elisa Souza

2011-01-01

This study evaluated the mechanical performance of teardrop-shaped loops and teardrop-shaped loops with helix used in orthodontic space closure. Sixty retraction loops made with 0.019" x 0.025" stainless steel (SS) and beta-titanium (BT) wires were used. They were attached to a testing machine to measure the magnitudes of the sagittal force and the load-deflection ratio necessary for 1 mm, 2 mm and 3 mm activation. The results demonstrated that the BT alloy presented significantly smaller mea...

Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines

Czech Academy of Sciences Publication Activity Database

Brahmkshatriya, Pathik; Dobeš, P.; Fanfrlík, Jindřich; Řezáč, Jan; Paruch, K.; Bronowska, A.; Lepšík, Martin; Hobza, Pavel

2013-01-01

Roč. 9, č. 1 (2013), s. 118-129 ISSN 1573-4099 R&D Projects: GA ČR GBP208/12/G016 Grant - others:Operational Program Research and Development for Innovations(XE) CZ.1.05/2.1.00/03.0058 Institutional support: RVO:61388963 Keywords : binding affinity * cyclin-dependent kinase 2 * QM/SQM/MM * PM6 * pyrazolo[1,5-a]pyrimidine * semiempirical quantum mechanics * scoring function Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.942, year: 2013

The clinical efficacy of 1 mm-slice CT of the middle ear

International Nuclear Information System (INIS)

Noda, Kazuhiro; Noiri, Teruhisa; Doi, Katsumi; Koizuka, Izumi; Tanaka, Hisashi; Mishiro, Yasuo; Okumura, Shin-ichi; Kubo, Takeshi

2000-01-01

The efficacy of the preoperative 1 mm-slice CT for evaluating the condition of the ossicular chain and the facial canal was assessed. CT findings were compared with the operative findings of middle ears in 120 cases of chronic otitis media or cholesteatoma that underwent tympanoplasty. The reliability of 1 mm-slice CT in detecting any defect of the ossicular chain was much superior to those of 2 mm-slice CT previously reported, and the difference between them is essential for preoperative information. On the other hand, thinner slice than 1 mm may be unnecessary, especially in routine use. (author)

The clinical efficacy of 1 mm-slice CT of the middle ear

Energy Technology Data Exchange (ETDEWEB)

Noda, Kazuhiro; Noiri, Teruhisa [Kawanishi Municipal Hospital, Hyogo (Japan); Doi, Katsumi; Koizuka, Izumi; Tanaka, Hisashi; Mishiro, Yasuo; Okumura, Shin-ichi; Kubo, Takeshi

2000-02-01

The efficacy of the preoperative 1 mm-slice CT for evaluating the condition of the ossicular chain and the facial canal was assessed. CT findings were compared with the operative findings of middle ears in 120 cases of chronic otitis media or cholesteatoma that underwent tympanoplasty. The reliability of 1 mm-slice CT in detecting any defect of the ossicular chain was much superior to those of 2 mm-slice CT previously reported, and the difference between them is essential for preoperative information. On the other hand, thinner slice than 1 mm may be unnecessary, especially in routine use. (author)

Influence of irradiation (Co60) in pre-implant rabbits embryos: effect on blastocyst diameters and embryos smaller than 2 mm

International Nuclear Information System (INIS)

Approbato, Mario S.; Oliveira Moura, Katia K.V. de; Souza Florencio, Rodopiano de; Cunha Junior, Carlos; Garcia, Ricardo; Faria, Renato S.; Benedetti, Leonardo N.; Goulart, Flamarion B.

1995-01-01

We studied the effect of ionizing irradiation on 12 New Zealand rabbits (65 embryos), in three different times: at match time (zero hour), two days after and four days after, with two different irradiation doses, 5 c Gy and 10 c Gy. Six rabbits (36 blastocysts) were used as controls. The matching instant was the zero hour. Exactly six days after (± 60 minutes) the embryos of each rabbit was picked up by flushing the uterus with culture media. The embryos were fixed in methanol for 48 hours, and colored with acid Mayer hematoxylin. The following embryos parameters were studied: diameter growth; percentage of embryos smaller than 2 mm. We observed that only the irradiation time influenced the blastocysts diameter (no irradiation dose). There was no relation between percentage of embryos smaller than 2 mm and the irradiation. (author)

Visceral angiography with intra-arterial DSA and a programmed 100 mm technique

International Nuclear Information System (INIS)

Triller, J.; Ackermann, B.; Jung, H.

1988-01-01

One hundred and seventy specially selected visceral angiograms were carried out of 96 patients using I-A DSA and 100 mm technique. 85.2% of the I-A DSA and 91.7% of the 100 mm images were of good quality. I-A DSA produced comparable or better quality than the 100 mm technique in 66% during the arterial phase, in 79% during the paranchymatous phase and in 70% during the venous phase. The 100 mm technique produced better quality in a third of the cases during the arterial phase and in a quarter of the cases during the parenchymal and venous phases. The indications for the 100 mm technique are failure of I-A DSA or the need for high spatial resolution. (orig.) [de

Elastic and inelastic processes in H+ + CH2 collisions below the 1.5 keV regime

International Nuclear Information System (INIS)

Suno, Hiroya; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.; Kimura, Mineo; Janev, R.K.

2005-01-01

Electron capture and direct elastic scattering in collisions of H + ions with CH 2 molecules between 0.5 and 1.5 keV are theoretically investigated. A molecular representation is adopted within a fully quantum-mechanical approach. Differential cross sections (DCSs) for elastic scattering and electron capture are calculated at 1.5 keV and 0.5 keV for different molecular orientations. Our results indicate that electron capture dynamics and corresponding electron-capture cross sections depend substantially on the molecular orientation, thus revealing a strong steric effect. (author)